Merge returning non existent values

The cause of your issue is a known phenomenon: if you sort a table and then use Table.GroupBy or Table.Distinct with the sorted table as source, the sort order is not necessarily maintained.

In your case, it means that the nested tables can have a different sort order then the original table.

Apparently you can even have different results in different queries.

The solution is to buffer the sorted table:

    #"Sorted Rows" = Table.Buffer(Table.Sort(#"Replaced Values1",{{"HcmWorker_FK_PersonnelNumber", Order.Ascending},{"StartDateLeave", Order.Descending},{"EndDate", Order.Descending}})),