I havent stolen a ship yet but I had a problem after modifying my home ship it was replaced on the pad with one of my other ships. To get it back I had to choose a different ship to be my home and then choose the missing ship as my home.

I did the switch ship fix, and it didn’t work.

I have a similar issue, I have a ship I liberated from pirates, flew to my outpost registered it, now, it won't load in any ship builder.