The Fantasy Flight Games rule book addresses this in multiple locations
Stripping a Planet of Ships
As soon as a player removes the last of his or her ships from any planet, that player no longer has a colony on that planet. Any ships involved in the encounter cannot return to that planet. Ships retrieved from the warp cannot return to that planet. That player has no colony there. If a player has no ships left on one of his or her home planets, he or she must still defend it (with zero ships). If a situation arises where a player must relocate ships but he or she has no colonies anywhere on the board, those ships go to the warp. (Pg. 12)
Throughout the game, ships will go to the warp when encounters are lost. At the start of an encounter, one of the offense’s ships is retrieved from the warp and placed in one of his or her colonies (home or otherwise). If a player has no colonies, the retrieved ship is placed directly in the hyperspace gate. (Pg. 7)
The FAQ covers what to do if a Mobius Tubes is used.
Q: How does Mobius Tubes work if you have no planets?
A: Your ships exit the warp, then any ships that have no colony to return to are returned to the warp. If you are the offense, you may place up to four of your ships in the hyperspace gate before the others are lost to the warp.