Column disappears after adding custom columns

Hi there,

I'm fairly new to Power Query, but have been learning lots with the help of a coworker who is a power user, so forgive me if this is a dumb question.  I am currently building some files that have a circular reference to each other:

User 1 enters data in File 1

File 1 feeds File 2.  User 2 enters data in blank cells in File 2.

File 2 feeds back to File 1 (via table lookups).

"File 2" is referencing a snapshot of the table in File 2 so that any data entries User 2 made to the file are preserved when the document is refreshed.  Here is a quick summary of the process:

 -load snapshot of table to query,

 -merge back to original table

 -add in custom columns with "if" statements

 -delete original and merged "snapshot" columns

 -rename custom columns to original column names

 -reorder columns so that the output matches the original table layout. 

I have used this structure before without issue, but am now having a problem where an unrelated column is disappearing after I add my last custom column.  The error is telling me that the missing column was not found on the "snapshot" file, but I'm puzzled by this for two reasons:

1) when I check the snapshot the column is there

2) this column was not one that was included when I expanded columns after merging, so why does it even matter?

Im totally stumped.  Any help is greatly appreciated!