Sounds like, just as can happen with damaged FileMaker files, that the repaired Excel file is not fully repaired and thus the damage repeats. You may need to try replacing this file with a completely new copy un less I am misunderstanding how you are creating this file.
i had suspected that the problem was at the Excel end and had already done exactly what you suggest - trash the Excel file and start again. However the problem still reoccurs, and the new file is good for a couple of closes & re-openings, and will then become corrupted.
I am now suspicious of MSQuery and the refresh process. It takes quite a long time to get the data over ODBC (almost 30 seconds on my i7 Macbook whcih seems like about a week!) and I am trying to eliminate possible causes of error like a background refresh that gets interrupted somehow.
You might want to post a description of this issue over in Report an Issue as a possible bug. The techs that monitor that section may know something useful here.