Power Query for Workbook Merge

aflintdepm 

You're not Merging files but Combining files and the process you use works very well. Until your scary #"Filtered Rows" it's a pretty classic combining query where PQ very rarely makes mistakes not to says never. Looking at your code there are a couple of unecessary steps (leads to inefficiency) and if I made no mistake it can be shortened as:

let
    Source = Folder.Files("C:\Users\svc_apps\xxxxxxxxx\xxxxxxxxxxxxx\Data Downloads\Marketing Report File Download"),
    #"Filtered Hidden Files1" = Table.SelectRows(Source, each [Attributes]?[Hidden]? <> true),
    #"Invoke Custom Function1" = Table.AddColumn(#"Filtered Hidden Files1", "Transform File", each #"Transform File"([Content])),
    #"Renamed Columns1" = Table.RenameColumns(#"Invoke Custom Function1", {"Name", "Source.Name"}),
    #"Removed Other Columns1" = Table.SelectColumns(#"Renamed Columns1", {"Source.Name", "Transform File"}),
    #"Expanded Table Column1" = Table.ExpandTableColumn(#"Removed Other Columns1", "Transform File",
        Table.ColumnNames(#"Transform File"(#"Sample File"))
    ),
    #"Removed Columns" = Table.RemoveColumns(#"Expanded Table Column1",{"Source.Name"}),
    #"Removed Top Rows" = Table.Skip(#"Removed Columns", 2),
    #"Promoted Headers" = Table.PromoteHeaders(#"Removed Top Rows", [PromoteAllScalars=true]),
    #"Changed Type" = Table.TransformColumnTypes(#"Promoted Headers",
        {
            {"Branch", type text}, {"MR", Int64.Type}, {"First Name", type text}, {"Middle Initial", type text}, {"Last Name", type text},
            {"Status", type text}, {"Referral Date", type date}, {"Primary Insurance", type text}, {"Physician First", type text},
            {"Physician Last", type text}, {"Internal Referral First", type text}, {"Internal Referral Last", type text},
            {"External Referral", type text}, {"Case Manager", type text}, {"Start of Care Date", type date}, {"Episode Start", type date},
            {"EpisodeEnd", type date}, {"Episode Length", Int64.Type}
        }
    ),
    #"Filtered Rows" = Table.SelectRows(#"Changed Type", each
        (
            [Branch] <> "Branch" and
            [Branch] <> "Generated on 06/20/2023 06:52 by xxxxxxxxx" and
            [Branch] <> "Generated on 06/20/2023 06:53 by xxxxxxxxx" and
            [Branch] <> "Generated on 06/20/2023 06:54 by xxxxxxxxx" and
            [Branch] <> "Generated on 06/20/2023 06:55 by xxxxxxxxx" and
            [Branch] <> "Generated on 06/20/2023 06:56 by xxxxxxxxx" and
            [Branch] <> "Generated on 06/20/2023 06:57 by xxxxxxxxx" and
            [Branch] <> "Generated on 06/20/2023 06:58 by xxxxxxxxx" and
            [Branch] <> "Generated on 06/20/2023 06:59 by xxxxxxxxx" and
            [Branch] <> "Generated on 06/20/2023 07:00 by xxxxxxxxx" and
            [Branch] <> "Recert by Episode Start Date: 06/20/2023"
        ) and ([Status] = "Active")
    )
in
    #"Filtered Rows"

Given you can't share anything a suggestion, tempo.:
#1 Delete step #"Removed Columns"
#2 After the #"Changed Type" step Add a new one to rename the 1st column Source.Name

this will help you identify where the duplicates come from

Thanks. I see this is can only be troubleshooted with a couple of the source files. Or a screen-share where we walk through the steps. I'm afraid I don't have the time for this at the moment.