Query editor loads same files multiple times

I would give a strategically place Table.Buffer a try (sorry if this has already been mentioned):

#"Merged Queries" = Table.NestedJoin(Table.Buffer(#"Removed Columns"), {"UsageWeekNo"}, Sheet2, {"yrmth"}, "Sheet2", JoinKind.LeftOuter),

let
Source = Folder.Files("C:\...\PowerBI\FC"),
#"Filtered Hidden Files1" = Table.SelectRows(Source, each [Attributes]?[Hidden]? <> true),
#"Invoke Custom Function1" = Table.AddColumn(#"Filtered Hidden Files1", "Transform File (5)", each #"Transform File (5)"([Content])),
#"Renamed Columns1" = Table.RenameColumns(#"Invoke Custom Function1", {"Name", "Source.Name"}),
#"Removed Other Columns1" = Table.SelectColumns(#"Renamed Columns1", {"Source.Name", "Transform File (5)"}),
#"Expanded Table Column1" = Table.ExpandTableColumn(#"Removed Other Columns1", "Transform File (5)", Table.ColumnNames(#"Transform File (5)"(#"Sample File (5)"))),
#"Changed Type" = Table.TransformColumnTypes(#"Expanded Table Column1",{{"Source.Name", type text}, {"SupplierCode", type text}, {"SupplierName", type text}, {"DockCode", type text}, {"TransmissionDate", type date}, {"PartColourCode", type text}, {"PartDesc", type text}, {"KanbanNo", Int64.Type}, {"PartNo", type text}, {"OrderLot", Int64.Type}, {"UsageWeekNo", type text}, {"UsageDate", type date}, {"TotalPCS", Int64.Type}, {"LastManifest", type any}, {"LeftToOrder", type any}}),
#"Removed Columns" = Table.RemoveColumns(#"Changed Type",{"SupplierCode", "SupplierName", "PartColourCode", "LastManifest", "LeftToOrder"}),
#"Merged Queries" = Table.NestedJoin(Table.Buffer(#"Removed Columns"), {"UsageWeekNo"}, Sheet2, {"yrmth"}, "Sheet2", JoinKind.LeftOuter),
#"Expanded Sheet2" = Table.ExpandTableColumn(#"Merged Queries", "Sheet2", {"Mondays"}, {"Sheet2.Mondays"}),
#"Removed Blank Rows" = Table.SelectRows(#"Expanded Sheet2", each not List.IsEmpty(List.RemoveMatchingItems(Record.FieldValues(_), {"", null})))
in
#"Removed Blank Rows"