[MoP] Pet bar abilities missing and won't save

So I've had a ongoing issue with abilities of my pet bar disappearing and then not be able to be added back. It's rendered 2 of my spirit beasts almost unusable so far (no stances on either and no attack on one). You can drag the abilities back while the pet is summoned but they disappeared as soon as it despawns, you log out, teleport or dismiss the pet. I've tried many different "fixes" including placing the ability and then dismissing and relogging, changing positions of abilities and even doing the regular clearing cache and disabling addons.

From my reading the bar is saved server side and a GM suggested a few months ago when I made a ticket about the issue that it was a bug. Is there any way to fix this apart from wasting days trying to retame spirit beasts (for it to just happen again)?