I know this is definitely a convoluted way to do it, but ...
1) Do a ful backup
2) Restore to a clean system archive system (ie total separate version of Jira just for this purpose)
3) Delete all projects you do not want from within Jira.
4) Backup the archive system which now gives you just the projects you want backed up.
5) clean out the archive system and shut it down until it is needed again.
This process could be scripted
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