It's kind of the point of those ships to not just be (re-)buildable... In my longer playthroughs I usually just phased out the NX-01 in the TMP-eras, and had it sit somewhere in my very core-systems for the remainder of the game from that point on.

What would be cool though, would be the ability to appoint flagships in a limited fashion, allowing for bonuses that depend on the shipclass the ship you chose is from. So if you lose the Enterprise for instance, you could appoint a different "hero"/flagship of sorts.

When my NX-01 refit Enterprise got destroyed in some battle I got an event a few months later asking me if I wanted to rebuild it I don't know if the other Enterprises also get this event though.

Edit: As a result of the latest update to the mod they overhauled the ship designer making all (so far Human/Federation only) ship designs their own ship classes but so as not to clutter the ship designer and ship build menu ship designs get automatically retired, I assume when certain techs get researched, but you can recommission them if you build the Starfleet Naval Museum.

Thank you for your helpful answers, guys. I was a bit impatient it seems, since I got the event to rebuild the enterprise after a while. As for the recomissiong of the ship designs: How exactly does that work? I built the Fleet Museum, do I have to use it somehow? I can't chekc that right now, but will do so when I'm home again.

Once you build the Starfleet Naval Museum you could be able to click on their flag to open communications with them, kinda like clicking the flag next to another empires planet opens the communications screen with that empire. You should then have a few buttons to select to the following effect:
What is the Starfleet Historical Society?
Show 'Frigate' classes.
Show 'Cruiser' classes.
Show 'Explorer' classes.
etc.
Then you select the class of ship you want to recommission, I think the Intrepid is under the Cruiser category so you would select Show 'Cruiser' classes. You should then get a set of new buttons, all in pairs with one being to recommission a ship class and the other being to retire that ship class. Just select the recommission xyz ship class. Their is a limit to the number of ship classes you can recommission, I don't know if this number increases as time goes on but I am limited to 4 right now in my current save.

Also I haven't actually recommissioned any ships yet but I would assume they have the same weapon selection limitations when recommissioned as when that ship class was considered new. So for example I don't think you will be able to equip anything better then the ENT era weapons on the Intrepid-class, though I think you can still slap a TNG era warp core in it somehow.

Works just as described, thank you. Never occured to me to interact with them as if they were a different nation.

Uhm, before I open another thread for this. I researched something called a spore-drive and thought I could finally be rid of the pseudo-warp-drive, at least for while ^^. Unfortunately I cannot equip it on my ships. I guess the UFP can't use them?

Originally posted by BKL Zirial:

Works just as described, thank you. Never occured to me to interact with them as if they were a different nation.

Uhm, before I open another thread for this. I researched something called a spore-drive and thought I could finally be rid of the pseudo-warp-drive, at least for while ^^. Unfortunately I cannot equip it on my ships. I guess the UFP can't use them?

Experimental drives, ie. Spore drive and Transwarp drive, can only be used on the Advanced Cruiser classes, ie. the Crossfield and Excelsior classes. I am not sure if their is another one after the Excelsior though.
In previous versions of this mod you could use the spore drive on all ship classes allowing you to have Galaxy classes jumping around like they had a jump drive from the vanilla game equipped.