I removed mine, but I don't think I wrote about it. No particular gotchas in my case. Basically there are three different things.
1) Larger central hole where shaft goes through (maybe 1-1/4" in diameter.
2) Smaller hole where cable goes through (maybe 1/2" in diameter).
3) Horseshoe of smaller holes where "pointy" screws held base to roof.
Removing was straightforward as I remember it.
I chamfered and then patched the horseshoe of screw holes with neat, then thickened epoxy. These holes are small so don't need patches other than the thickened (with structural filler such as colloidal silica or structural thickener powder). I won't go into detail yet in case you already know epoxy or plan to do something else. This can be gelcoated or painted over after the epoxy has time to cure (I use tape to protect it from UV during this time period, as epoxy is vulnerable to UV).
The two larger holes I thought I would probably use for running solar cables into the rig, so I "temporary long term" patched them with watertight but easily removable patches. These consist of circles cut out of thickish galvanized flashing (bought in ~30" x 36" sheets at Home Depot), and affixed with butyl tape. They have held up incredibly well and no leaking, yet easily removable and a bit of mineral spirits cleans it up without undue hassle.
Here are two photos of the roof after I epoxy filled the smaller holes and "long term temporary" patched the two larger ones. As you can see the epoxy filled holes are completely flush once trimmed (sharp chisel during green stage). The one galvanized patch I have not rolled down yet, so you can see it sticking up slightly. The solar down wire fitting I'm planning to use will fit the original larger hole so there will be no more patch, and then presuming I don't use the smaller/larger hole, I'll patch that as well (for real with fiberglass/epoxy).
The reason I use epoxy resin (as opposed to polyester, with which our rigs were built) is that polyester has poor secondary bonding characteristics, while epoxy has excellent ones. Anything added after the day it was built is a secondary bond (no more chemical linking possible after the resin cures), so that's important. Vinylester would also work well, but I use epoxy a lot for boat repair so have it on hand (and I don't like the smell of the "esters").
Epoxy will also form a primary [chemical] bond, but only while in the green stage (so new work done in layers can be primarly bonded to itself, but will always be a secondary [mechanical] bond to the original substrate, so a good secondary bonding characteristic is important (which polyester is not so good at). Once repaired with epoxy, it's basically as strong/stronger than new.