We’re working on resolving the issue on EFI boot entries getting cleared before we deploy through LVFS. We are exploring also releasing through LVFS, but in a way where manual running an update is possible rather than enabling updates automatically to avoid someone getting their EFI boot entries cleared unexpectedly.
In the meantime, you can use the manual method with a USB flash drive updater: Framework Laptop BIOS and Driver Releases
On Fedora and Ubuntu, this should (based on my recollection) work without EFI boot entries getting cleared.