Unfortunately, I believe ships you get as you level up require you to buy them back with Dilithium at the Shipyard if you decommission them. They cost anywhere up from 8,000 to 120,000 Dilithium.
Member since November 2009... I think. (UFP) Ragnar
The free ships from levelling can't be reclaimed for free (they can be re-purchased with lots of dilithium). However, since they are of lower tier, they're also significantly weaker... except for the T1 ships and the Connie Refit (and several of the KDF ships), if you really want to keep those old ships around, go ahead and buy the Retrofits from the Fleet store. They cost a lot of Fleet Credits (200k each), but they are more viable choices for those old-ship models.
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(UFP) Ragnar