So this isn’t a hypothetical. There’ve been numerous reports of reputations reset to Neutral since 11.0. These are separate from the display issues which were being reported on just after the patch - the reputations are actually functionally reset to neutral.
The most acknowledgement we’ve gotten of this issue is a bullet point in a support article:
A situation where reputations which have a direct correlation on the opposite faction (such as Battlegrounds factions) are reset to neutral. A hotfix is planned for this issue and it should be resolved for players logging in after that fix soon. Investigations are ongoing for players who experienced the issue and need their reputations fixed.
This was over a month and a half ago, and I’m not aware of any updates. The bug causing resets may have been fixed, but as far as I know, missing reputations haven’t been restored.