Greeting,
It is not a supported refit to do this and still have the unit be an Omni. Fixed equipment on an OmniMech can only be changed by making is a custom, non-Omni design. At that point it would be a normal refit of the unit, but the freed space would not be an Omni pod.
This has occurred once or twice in canon design, where a Clan custom has been made from an Omni and becomes a Non-Omni.
Best,
Joel BC