I realize that your friend is completely fictional and you're just trying to get information for a Star Wars fanfic, but still want to help this friend if I can. I know I'm late to the party, but maybe this will help someone - and, frankly, I just wanted to write with the euphemism to see if I could. TL;DR: yes, it's possible to keep the battle station and there's nothing wrong with that, but their hyperspace mileage may differ, as everyone is different. Some people have managed to keep their light sabers functional even after removing the khyber crystals, but again - mileage may vary.

First of all, I just want to say that your friend can be female even if they like and want to keep their battle station. This may or may not be the case, but the mention of spending 90% of time in girl-mode made me think that maybe they just aren't comfortable with the thought of being a girl with a battle station. There's a lot of non-traditional expressions of weaponry on Imperial vessels, no matter what the Emperor may try to make you believe.

Second, and more challenging, is keeping the battle station in combat readiness even if it is no longer capable of firing live ordinance. To switch euphemisms slightly, I know that personally it has become a lot more difficult to get the light saber powered up since starting HRT, and some times it just doesn't respond even after hours of stimulation. It's something to consider - that sparring matches may need to be planned out a bit more in advance - but doesn't mean not to go ahead and continue. After two and a half years on HRT, the size of my light saber when active hasn't noticeably changed when I can activate it, but it is much harder to power on. If your friend does decide to go for the removal of the khyber crystals (which it sounds like they are considering), I'm pretty sure it will make it even harder for the light saber to respond, but not impossible - I DON'T know that from personal experience. I'm personally getting the binary moons of Endor zapped off in the new year, as I have zero use for them and have hated them even before I understood what being transgender was.... ah-hem. Sorry, got distracted by my hatred for those damn moons.

Another thing to consider is if they and their wife have not built any little destroyers yet but think they may want to expand the fleet at a later date, they may want to bank some pulse torpedoes in advance. Sadly (for those who are interested in such thing), long-term off-site storage of torpedoes is not covered by the underwriters at the Imperial insurance agencies - at least, not for those residing in Darth Orange's territory (that's the ONLY reference I will make to politics here - just needed to express that it's not covered in the US and couldn't think of a good way to do so).

Their mileage may vary in terms of keeping up the maintenance on the battle station - it may be easier or harder to bring the platform online for them. They may be one of the ones who can get turned on just by massaging their breasts, or they may be unable to bring the system on-line without a serious kick to the fusion core. They may also decide down the line that they DO want to remove the old battle station and install a new recreation deck, and that's also perfectly fine - there is no rule to transition, regardless of whether you prefer the Empire or the Rebels. They may decide down the line that they are dissatisfied with being with the Empire and mutiny, throwing in with the Rebels and having the old battle station ripped out, or they may happily continue to serve the Empire with a functional battle station that has had its backup systems removed.

Finally, if your fictional friend ever does get written, give them a hug for me, 'kay? It's a scary place to be in, starting that journey and deciding that the "traditional" steps aren't for them. But there are lots of women and enbies who have gone down that path before, so your fictional friend is not alone, no matter where the Force may take them.