Power Query Not Loading All Rows

Hey sorry I am pretty new to this whole BI thing and am entirely self taught. So what I have probably looks pretty ugly. Also, I am not entirely sure which code you are asking for so I just copied what was in the advanced editor. I have 4 seperat queries that I have merged into a single query. I will paste what was done after. Please let me know if you were asking for something else. Thank you for your help.

let

    Source = SharePoint.Files("XXXXXXXXXXXXXXXXXXXXXXX", [ApiVersion = 15]),

    #"Filtered Rows" = Table.SelectRows(Source, each Text.Contains([Name], "Master Drug List")),

    #"Filtered Hidden Files1" = Table.SelectRows(#"Filtered Rows", each [Attributes]?[Hidden]? <> true),

    #"Invoke Custom Function1" = Table.AddColumn(#"Filtered Hidden Files1", "Transform File from NDCs", each #"Transform File from NDCs"([Content])),

    #"Renamed Columns1" = Table.RenameColumns(#"Invoke Custom Function1", {"Name", "Source.Name"}),

    #"Removed Other Columns1" = Table.SelectColumns(#"Renamed Columns1", {"Source.Name", "Transform File from NDCs"}),

    #"Expanded Table Column1" = Table.ExpandTableColumn(#"Removed Other Columns1", "Transform File from NDCs", Table.ColumnNames(#"Transform File from NDCs"(#"Sample File"))),

    #"Changed Type" = Table.TransformColumnTypes(#"Expanded Table Column1",{{"Source.Name", type text}, {"Product", type text}, {"NDC", type text}, {"Med Type", type text}, {"Category", type text}, {"Special Naming", type any}}),

    #"Removed Columns" = Table.RemoveColumns(#"Changed Type",{"Source.Name"})

in

    #"Removed Columns"

let

    Source = SharePoint.Files("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX", [ApiVersion = 15]),

    #"Filtered Rows" = Table.SelectRows(Source, each Text.Contains([Name], "Insurance - CPC Master List")),

    #"Filtered Hidden Files1" = Table.SelectRows(#"Filtered Rows", each [Attributes]?[Hidden]? <> true),

    #"Invoke Custom Function1" = Table.AddColumn(#"Filtered Hidden Files1", "Transform File from ThirdParties", each #"Transform File from ThirdParties"([Content])),

    #"Renamed Columns1" = Table.RenameColumns(#"Invoke Custom Function1", {"Name", "Source.Name"}),

    #"Removed Other Columns1" = Table.SelectColumns(#"Renamed Columns1", {"Source.Name", "Transform File from ThirdParties"}),

    #"Expanded Table Column1" = Table.ExpandTableColumn(#"Removed Other Columns1", "Transform File from ThirdParties", Table.ColumnNames(#"Transform File from ThirdParties"(#"Sample File (2)"))),

    #"Removed Columns" = Table.RemoveColumns(#"Expanded Table Column1",{"Source.Name"})

in

    #"Removed Columns"

let

    Source = SharePoint.Files("XXXXXXXXXXXXXXXXXXXXXXX", [ApiVersion = 15]),

    #"Filtered Rows" = Table.SelectRows(Source, each Text.Contains([Name], "PrescriptionFillLogReport")),

    #"Filtered Hidden Files1" = Table.SelectRows(#"Filtered Rows", each [Attributes]?[Hidden]? <> true),

    #"Invoke Custom Function1" = Table.AddColumn(#"Filtered Hidden Files1", "Transform File from RxFillLog", each #"Transform File from RxFillLog"([Content])),

    #"Renamed Columns1" = Table.RenameColumns(#"Invoke Custom Function1", {"Name", "Source.Name"}),

    #"Removed Other Columns1" = Table.SelectColumns(#"Renamed Columns1", {"Source.Name", "Transform File from RxFillLog"}),

    #"Expanded Table Column1" = Table.ExpandTableColumn(#"Removed Other Columns1", "Transform File from RxFillLog", Table.ColumnNames(#"Transform File from RxFillLog"(#"Sample File (3)"))),

    #"Removed Columns" = Table.RemoveColumns(#"Expanded Table Column1",{"Source.Name"}),

    #"Promoted Headers" = Table.PromoteHeaders(#"Removed Columns", [PromoteAllScalars=true]),

    #"Filtered Rows1" = Table.SelectRows(#"Promoted Headers", each not Text.Contains([#"Fill #"], "Fill #")),

    #"Removed Columns1" = Table.RemoveColumns(#"Filtered Rows1",{"Pt Name", "Product", "Dosage Form", "NDC", "Sch", "CS #", "DE Init", "Disp Init", "Ver Rph", "TP ID", "Tot Amt Due", "Pt Amt Due", "Cost"}),

    #"Added Custom" = Table.AddColumn(#"Removed Columns1", "Fill IDs", each Text.PadStart(Text.From([#"Rx #"]),7,"0")&Text.PadStart(Text.From([#"Fill #"]),2,"0")),

    #"Changed Type" = Table.TransformColumnTypes(#"Added Custom",{{"Written Date", type date}, {"Fill Date", type date}, {"Fst Fill Date", type date}, {"Wqty", type number}, {"Dqty", type number}, {"RA", type number}, {"RR", type number}}),

    #"Removed Duplicates" = Table.Distinct(#"Changed Type", {"Fill IDs"})

in

    #"Removed Duplicates"

let

    Source = SharePoint.Files("XXXXXXXXXXXXXXXXXXXXXXXXXXX", [ApiVersion = 15]),

    #"Filtered Rows" = Table.SelectRows(Source, each Text.Contains([Name], "CloseOfBusinessDetailReport")),

    #"Filtered Hidden Files1" = Table.SelectRows(#"Filtered Rows", each [Attributes]?[Hidden]? <> true),

    #"Invoke Custom Function1" = Table.AddColumn(#"Filtered Hidden Files1", "Transform File from MasterTable-COB", each #"Transform File from MasterTable-COB"([Content])),

    #"Renamed Columns1" = Table.RenameColumns(#"Invoke Custom Function1", {"Name", "Source.Name"}),

    #"Removed Other Columns1" = Table.SelectColumns(#"Renamed Columns1", {"Source.Name", "Transform File from MasterTable-COB"}),

    #"Expanded Table Column1" = Table.ExpandTableColumn(#"Removed Other Columns1", "Transform File from MasterTable-COB", Table.ColumnNames(#"Transform File from MasterTable-COB"(#"Sample File (4)"))),

    #"Removed Columns" = Table.RemoveColumns(#"Expanded Table Column1",{"Source.Name", "store_num", "generic", "Billing_Method", "SERVICE_BILLING_INDICATOR", "Partial_Fill_Seq", "Prior Auth"}),

    #"Changed Type" = Table.TransformColumnTypes(#"Removed Columns",{{"Sold Date", type date}, {"Date_of_Service", type date}, {"Adjudication_Complete", type date}, {"QTY", type number}, {"TP_Total_Amt_Paid", Currency.Type}, {"PT_Pay_Amt_Total", Currency.Type}, {"Total_Claim_Price", Currency.Type}, {"acq_cost", Currency.Type}, {"Gross_Amount_Due", Currency.Type}}),

    #"Added Custom" = Table.AddColumn(#"Changed Type", "Fill IDs", each Text.PadStart(Text.From([rx_number]),7,"0")&Text.PadStart(Text.From([refill_num]),2,"0")),

    #"Merged Queries" = Table.NestedJoin(#"Added Custom",{"NDC_num"},NDCs,{"NDC"},"NDCs",JoinKind.LeftOuter),

    #"Expanded NDCs" = Table.ExpandTableColumn(#"Merged Queries", "NDCs", {"Med Type", "Category", "Special Naming"}, {"Med Type", "Category", "Special Naming"}),

    #"Renamed Columns" = Table.RenameColumns(#"Expanded NDCs",{{"Category", "Med Category"}, {"Special Naming", "Special Med Naming"}}),

    #"Merged Queries1" = Table.NestedJoin(#"Renamed Columns",{"TP_Name"},ThirdParties,{"TP_Name"},"ThirdParties",JoinKind.LeftOuter),

    #"Expanded ThirdParties" = Table.ExpandTableColumn(#"Merged Queries1", "ThirdParties", {"Coupon?", "Comm/Mcaid/Mcare"}, {"Coupon?", "Comm/Mcaid/Mcare"}),

    #"Renamed Columns2" = Table.RenameColumns(#"Expanded ThirdParties",{{"Coupon?", "Third Party Type"}, {"Comm/Mcaid/Mcare", "Third Party Category"}}),

    #"Merged Queries2" = Table.NestedJoin(#"Renamed Columns2",{"Fill IDs"},RxFillLog,{"Fill IDs"},"RxFillLog",JoinKind.LeftOuter),

    #"Expanded RxFillLog" = Table.ExpandTableColumn(#"Merged Queries2", "RxFillLog", {"Pt Address", "Wqty", "Dqty", "RA", "RR", "Presc Name", "Presc Address", "DEA", "Written Date", "Fill Date", "Fst Fill Date"}, {"Pt Address", "Wqty", "Dqty", "RA", "RR", "Presc Name", "Presc Address", "DEA", "Written Date", "Fill Date", "Fst Fill Date"}),

    #"Renamed Columns3" = Table.RenameColumns(#"Expanded RxFillLog",{{"Pt Address", "Patient Address"}, {"Wqty", "Written Quantity"}, {"Dqty", "Dispensed Quantity"}, {"RA", "Refills Allowed"}, {"RR", "Refills Remaining"}, {"Presc Name", "Prescriber Name"}, {"Presc Address", "Prescriber Address"}, {"Fst Fill Date", "First Fill Date"}, {"rx_number", "Prescription Number"}, {"refill_num", "Refill Number"}, {"Adjudication_Complete", "Adjudication Complete Date"}, {"QTY", "Quantity"}, {"NDC_num", "NDC"}, {"Patient", "Patient Name"}, {"TP_Code", "Third Party Code"}, {"TP_Name", "Third Party Name"}, {"COB_INDICATOR", "COB Indicator"}, {"TP_Total_Amt_Paid", "Total Amount Third Party Paid"}, {"PT_Pay_Amt_Total", "Total Amount Patient Paid"}, {"Total_Claim_Price", "Total Claim Price"}, {"acq_cost", "Acquisition Cost"}, {"Date_of_Service", "Date of Service"}, {"Gross_Amount_Due", "Gross Amount Due - incorrect do not use"}})

in

    #"Renamed Columns3"