We know the replicator can create matter from thin air. This is tried and tested technology even in the TNG era.
In a few episodes we have seen strange transporter effects e.g. duplicate Riker, Tuvix, suspended animation Scotty etc
Why not have a spacedock that scans and "beams up" say a runabout and then duplicates it? Obviously some materials can't be duplicated for example latinum, i'm not sure how many are used in starship design but then could probably copy and paste 80% complete shuttlecraft to their their hearts content, even duplicate defiants if they had mega -transporter-replicator copiers.
You could even have some crew members copied - need an expert on the Borg but Seven is unavailable? Copy her. Copy a team of her to populate a base full of anti-borg experts all working on new anti-borg technologies and tactics. Screw it you could even 'Tuvix' Seven and Picard (both borg experts), Seven and B'Ellana, Bones and Bashir, B'ellana and Geordi, B'ellana and Geordi and Scotty...
Need an experienced captain for a possible suicide mission? copy Picard.
The possibilities are endless.