A friend of mine uses My Boy, and I just helped him rename one of his saves to match a new version, so I can confirm: Yes, you will be able to continue playing, you just have to change the name of the .sav file to match the name of the new .gba file.
Example, just in case you are having trouble understanding:
Pokemon 2 Beta 2.gba has a .sav file with it named "Pokemon 2 Beta 2.sav"
After you update, the name is changed to: Pokemon 2 Beta 3.gba so you will have to rename the .sav file to "Pokemon 2 Beta 3.sav" and you will be able to continue right where you left off!