Don't think there is any util, etc. The way you are doing really might be the only/best way. However, depends upon if the bug required a lot a little. So keeping that in mind think I'd investigate ...
Downoad a 2.5 backup (which used zipping to archive)
Downoad a 2.9 backup (which uses tar.gz ).
Decompress them both in different directories.
Inspect the moodle_backup.xml file as well as other .xml's related to files ... in other words, compare the moodle_backup.xml file from a 2.5 backup to the moodle_backup.xml file of a 2.9 backup for differences.
One might be able to 'doctor' the 2.9 moodle_backup.xml file to make it compat with 2.5 restore.
When re-compressing the doctored 2.9 backup, use zip. 2.5 talked only zip. 2.6 was the first version to introduce the new compression ... gzip (tar.gz).
Actually, that might be all you need ... download backup of 2.9, uncompress, recompress using zip restore to 2.5.
'spirit of sharing', Ken