Building a TT bike with internal cables from new. It has the thin inner lining sticking out of each hole. Good so far. Now is this just used to thread the inners then pulled out ( and re-threaded if cables need changing or does it stay inside. And there it will stay when the cables are changed. I favour the former but stand to be corrected.

I would leave them there i think

Thing is, leaving them in means cutting to fit exactly to match the outers. That means they drop lose when the cable is removed. These inners are not fixed and are currently 5cm longer at each port than needed.
You may be right though. Any other votes?

Take them out after you’ve threaded the inner, then refit before you change cable. Helps if you tape them to the frame when changing inners in case you let go!

I guess that’s why there is some spare. To grab.

Take them out. When you change the cables, re-thread them over the old cable in-situ and tape them in place before removing the old cable.

EDIT: I appear to be repeating what has been said. Must be right then.