Once you've upgraded your ship and your SAIL has vanished, use these commands:
/admin
/spawnitem avalitechstation
/admin
Once done, place the tech station back where it was.(It will persist through upgrades just like every other object you place on the ship) (Of course, nothing is preventing you from placing it wherever you like.)

WHY:
When Chucklefish introduced SAIL's introductory speech, the Avali sail constantly skipped it. This is because SAIL used to be non-persistent, which means every upgrade it would get destroyed and remade in the same place. Interacting with SAIL the first time triggers not only his intro speech, but also an upgrade, so SAIL would start his speech for exactly one frame before being destroyed by the game engine and a new SAIL spawned in its place.

Now, SAIL is a persistent object, meaning it does not get destroyed between upgrades. However, in order to implement this, I had to remove the SAIL spawn point from every tier except the first.

Persistence is saved with the object when it is first created by the game, so because you had an old character from before this change, your SAIL station was set with the old flags (Meaning it was nonpersistent). So when you upgraded, your SAIL station (like before) was destroyed, only this time there was no spawn point for it in the new ship, so it does not spawn like it used to.