What constitutes losing omni capability exactly?
This is answered within the game rules (StratOps and the new CampOps). The
summary is that if you do anything to remove, replace, or modify (no, not repair, and not replace a destroyed component either) with any sort of fixed equipment on any Omni for any reason and in any circumstances at all, you lose Omni capability on that Mech forever. Pull the Jump Jets off a Summoner to add armor? No more Omni. Replace a torso jump jet with a medium laser? No more Omni. Take away a ton of pod space to up-armor a Hellbringer? No more Omni. Put an XL engine in an SFE Omni? No more Omni.
Replace a Jump Jet that got shot during a fight with a functional Jump Jet? Yes, you keep Omni capability, obviously.
In essence, Omnis trade complete freedom to screw around with their weapon and equipment loadout for being strictly unable to modify anything that isn't found inside the pod space. For the purposes of HM,WT, and
only for that purpose, I wrote a very limited and specific exception into our rules, which allows you to replace a piece of hard-mounted equipment with an item that takes up the same tonnage and same critical space (using the hard-mounted Avatar medium lasers in the CT as the example). That is a house rule for our campaign and this campaign only.