Sorry about the problem and frustration you’re having with upgrading.
I never used resources in earlier releases of RapidWeaver. The process of using a pointer to a file on your Mac instead of copying the resources into the project wasn’t a good design in my never humble opinion.
In RapidWeaver 8 RealMac did a complete redesign of how resources work. It’s a much better but not perfect solution. Unfortunately the conversion process from the older RW7 resources to the newer RW8 version hasn’t been a very clean process.
If you’re looking for a “fix” in this upgrade process, it’s probably not going to happen. I’m not trying to make excuses just being realistic. RapidWeaver 8 is getting long in the tooth and RW9 Probably isn’t far off. On top of that with each new release of MacOS the system is getting more and more locked down.
In your OP back in September of 2018 it was suggested to try an intermediate conversion to RW7 since you’re skipping a release:
You indicated that the resources didn’t work when you open the project in RW7? That’s usually, most people didn’t have that problem, but going from RW7 to RW8 was the messy part.
You indicated that you have thousands of resources, so I’d consider doing what Rob @Rovertek suggests and manage them outside of RapidWeaver. I think the new RW8 resource management is very stable and works well (once you get the resources converted) but managing that many files with it would be difficult.