Hello,
If you are still having problems with those .sql updates not being applied, you could do them manually in HeidiSQL or Navicat (haven't used) and it is a simple yet tedious process.
All of the missing files should have been automatically place in this folder
Code:
C:\<your server directory>\Source\utils\sql\git\required
"<your server directory>" is Akka's repack or w/e it is called. Hopefully the rest is accurate to that.
You can use the UI in either of the above programs to find and run the queries.
As far as backing up, I think it's great the repack comes with something. I also think learning how to do it on your own from K-Krabs suggestion is a good idea.
I'll stop there.