AAI's author at https://mods.factorio.com/mod/regenerate-terrain/discussion/5c997d56b9814e000de03745 explained that resources not regenerating with that mod should be fixed on RSO's side, so I'm reporting it here.

I can try to take a look but not sure if it can work 100%.
There is a bit of unhandled issue with RSO that ore patch might be generated on one chunk but cover neighbouring chunks. Handling it correctly is pretty much out of scope currently - would need to redo a lot of ore generation and remove some features.
And Regenerate Terrain mod does lots of map actions all at once - I have no idea how that will affect RSO generation.

I looked at the code and I know why I did not add support for deletion of chunks. It would require pretty complex tracking of chunks inside region and partial resource generation potentially.
Basic problem comes from the fact that deleting single chunks from region creates kind of holes and RSO would need to track them and try to regenerate resources inside them somehow. This could get pretty complex and I'm not planning to make such big changes to RSO currently.

So for now I'm affraid that RSO can be considered not compatible with "Regenerate Terrain" mod.

Ok, thanks for looking it up so quickly anyway. :)

Hmm and of course I forgot about the simpliest solution.
You can call /rso-regenerate after regenerating terrain to regenerate all the resources.
It has the drawback that it will recreate even ores that were mined. And it might create different layout that it was before - but should be pretty close.

Eh. That changes the picture a lot.