It doesn't tell you clearly, and yes, you might have 'hidden' loss.
I had that often in the last decades of working with Excel, and have stopped to ever use that function.
I recommend to read such messages as 'the file is corrupted, go find your last backup, or you will rue it later'.
Of course, if you don't have a backup, that is tough (it taught me to have backups). But continuing with a 'recovered' file, and finding months later that relevant data is missing, is often worse.
if the file is always generated that way, you don't have another option - take it and hope for the best. Aside from saving the result in a new file, and comparing the two with tools, there is no way to know if something was lost.
Note that *.xlsx is factually ZIP file - simply rename it to *.ZIP, and open it, and you can analyse all the pieces of the Excel sheet separately, in multiple sub-folder and (XML-)files. Maybe you can identify the problem point and fix it manually.