From my troubleshooting with my own mod, I just discovered the workshop is NOT intelligently updating current existing files from the looks of things with mods. I had updated Canna-Ark and it was showing old past version features/bugs.
This was after 3 hours of troubleshooting why my mod updates we’re not showing up in Local Play, but did in PIE.
Here’s my findings with Canna-Ark (this is an example that pertains to my mod specifically), maybe this will help you;
“Steamworkshop is being buggy with updating certain files. If you have problems with certain engrams not showing up from Canna-Ark, or missing features you are going to have to manually DELETE your mod folder (FROM ARK!!! NOT THE DEV KIT!!!) with this ID “481755557”, and then unsubscribe and re-subscribe to get the new changes. I don’t know why it’s doing this or being so finicky, but that was the fix for me.”
Only after deleting the mod folder & the mod file. And then Unsubbing and resubbing, did it work.
Not sure if this is the problem in your case, but I highly suggest trying this as its an easy attempted resolution with nothing to lose.