Yes, Pocket is not able to run GB games from SD to avoid piracy.
Migrating a project from GB Studio 2.0 to 3.0 can be a lot of works because it generally break a lot of stuff.
I created a fork a GB Studio 2 that export natively game in pocket file.
https://github.com/BestPig/gb-studio#analogue-pocket-export
So it should be easy to port your game without the pain of migrating to GB Studio 3.0 :)
If you have any issue with it, don't hesitate to contact me.