Porting tilemaps is time-consuming indeed if you don’t have a dedicated script. I don’t know if you’re switching from manual tiles to new auto-tile or old auto-tile to new auto-tile; I don’t see a conversion script for either just doing a quick search, and I don’t know how feasible that is.
If you really have too many maps it may be worth writing your own and distributing it to help other devs working on long-running projects; but if you’re switching from individual tiles to auto-tiles, that may be too hard, I myself have the same issue with PICO-8 native map vs a new 3rd party “PicoMap” that supports meta-tiles.
I have an older Godot 3 project but I didn’t have much to add so I decided to just keep it in Godot 3 (which requires a little mental gymnastic every time I switch from Godot 4), but for a bigger project like this it’s probably worth it. Good luck!