I've modified the fonts and made some other changes in my current installation (2.21). I presume installing 3.1 will overwrite any of them. Is there any way to preserve existing changes or do I need to search them out and make them again in 3.1

Version 3 would not overwrite anything of 2.x

Both the theme folder for the files ("atahualpa3" vs "atahualpa2") and the options names for the option table ("bfa_ata_...." vs "ata_...") are different.

You can install atahualpa 3 as another, new theme and run them side by side.

This means however that no options will be carried over from v2 to v3. You would have to configure Atahualpa 3 from the start.