Can I apply a VC save file to a randomised GB ROM?

[Maximumbeans]

I've been trying to marry a few things together here and I don't know if I just need to give up on what I'm trying to do.

Quickfire facts:

• I've got a save file for an in-progress playthrough of Pokemon Yellow on the legit eshop version.
• I've randomised a GB ROM for Yellow so that I can get trade evos through level up, and turned it into a CIA using NSUI.
• I tried to randomise a dump of my version of Yellow and put it back in its place using Zeta's guide but it didn't work with my existing save file (the game booted fine but there was no effect from the randomisation).

So, is there any way to apply the existing save file to the VC inject that I made, or do I just need to forget that file and start a new game on the randomised ROM in order to get the benefit? I saw an explanation that the randomisation applies to the ROM itself and not the save file, but I don't know if that means the save file will never have this modification now no matter what I do or if there's a trick I can use. Thanks!