Hi @PaulUnger,
Unfortunately the ~ symbol carries special meaning within the USFM standard and therefore we use it as prescribed here: Words and Characters — Unified Standard Format Markers 3.0.0 documentation
I would recommend switching to a different character such as a forward slash ‘/’ or something else which doesn’t carry meaning.
I’m guessing it would be easy enough to place a rule in the changes.txt file (as seen below, and accessible on the Advanced tab) to do this for you so that you don’t need to change your USFM just yet; but longer term, I would encourage you to use some other character, otherwise you may trip up other software later down the track (DBL etc).
'~' > '/'