Should there be any problem when upgrading to R5.5 from R5F1? I assume since the backup format is the same as in R5F27 it should be fine, but I would like to check before something goes crazy.

Should work, but hasn't been tested that I'm aware of, although mjl did do one upgrade from something like R5A16...

I only test upgrades from the last milestone to the in-progress version, so I can only confirm that R5F27 -> R5.5 upgrades work. As tjc said, it should work to upgrade from R5F1, but you may need to keep your backup in place and do an upgrade to R5F27 and then to R5.5 if things go peculiar. mjl did do a lot of upgrades to R5.5 release candidates from ancient versions of KnoppMyth (IIRC, some of them unreleased milestones) but he also had some problems that others didn't have. You may want to PM him and ask if he did an R5F1 -> R5.5 upgrade.

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I tried it out and it worked fine. Everything seems to work OK.

As it should. You should be able to auto upgrade between any release between Release 4 and Release 5.5. The only issue is some items may have changed? Such as ivtv...