libstore/local-store.cc has the following comment:

void LocalStore::registerValidPaths(const ValidPathInfos & infos)
{
     /* SQLite will fsync by default, but the new valid paths may not be 
fsync-ed.
      * So some may want to fsync them before registering the validity, 
at the
      * expense of some speed of the path registering operation. */
     if (settings.syncBeforeRegistering) sync();

     [...]
}

However, currently sync-before-registering is set to 'false' AFAICT.  I 
think this might be the cause of bugs like 
<https://issues.guix.gnu.org/58013> (‘Can't use "guix pull"’), and maybe 
<https://issues.guix.gnu.org/57838> (‘failing to boot, probably due to 
guix gc’).

As such, I think we need to set it to 'true' by default instead.  Or if 
that turns out to be too expensive, instead do a recursive 'fsync' on 
the 'paths' (store items) that are about to be registered (and maybe 
some other tricks like disabling the 'fsync/sync' for most tests).

(Unverified if this solves those issues, just an idea ...)

Greetings,
Maxime.