When upgrading to a new version of android it can be difficult and complex. Particularly if you are no longer familiar with the project.
The android directory has 45 files and 37 directories. The ios directory has 42 files and 13 directories.

I would typically check these entire directories into git, and then when a new version of android comes out it can get quite difficult.
You can delete those directories and then do flutter create .
But then you have to find and merge the files within those directories which changed. Many of the files will have changed during the version bump and you have to try to figure out which of the few files (probably AndroidManifest.xml) which have changed.

It might be easier if there was a separate (maybe .android & .ios) directory where all of these files are stored. Then the android and ios directories would only contain the specific files you have changed (but in the correct location in the directory tree). Then, during build those changed files could be copied into the .android and .ios directories for building.
That way you can safely check in the android and ios directories and they will be sparse with just a couple of changed files. Then, when a new version of ios or android comes out you could just delete the .android and .ios directories and it should work right away.

The .android / .ios directories could even be uncompressed zip files with the complete version number attached, allowing swapping different versions of android in/out at will.