I think this was introduced during the sov update or later. Assuming it hasn’t changed, any time you hit save in the sanctum editor, it will break the rerun file. Here is when I reported this, so hopefully they have a fix in dev. I haven’t checked if it’s fixed on test.
When I’m doing sanctum edits, I keep a copy of the fixed version of the file open and re-save it after every sanctum edit save.