Power Query losing Columns

Max_Mustermann 

In case of csv check Transform Sample File query, first step looks like

= Csv.Document(Parameter1,[Delimiter=";", Columns=10, Encoding=65001, QuoteStyle=QuoteStyle.None])

Change Columns=10 on Columns=20 or like, i.e. max possible number of columns.

When in combined file remove all columns with no data. As variant that could be function which removes all empty rows and columns as

(Source as table) as table =>

let
    RemoveEmptyColumns = Table.SelectColumns(
        Source,
        List.Select(
            Table.ColumnNames(Source),
            each List.NonNullCount(Table.Column(Source,_)) <> 0
        )
    ),
    RemoveEmptyRows = Table.SelectRows(
        RemoveEmptyColumns,
        each not List.IsEmpty(List.RemoveMatchingItems( Record.FieldValues(_), {"", null} ) )
    )
in
    RemoveEmptyRows

Not sure about PDF, check the connector options if something similar.