Does it really require you to spend it permanently?
The way I experienced it is, that the game requires you to have the ressources for building the ship new, but it won't increase the usage once you upgraded. Example: I ahve my arch dreatnought which requires 4 thullium and one elerium. Now I make a version with upgraded weapons (no additional ressource cost). In order to be allowed to upgrade I ahve to have the ressources I would spent on building the new version (4 thullium one elerium). However once upgraded the ship still only costs 4 thullium 1 elerium and I don't have double the ressources invested.
I guess mechanicly the game builds the new version (carries over exp) for which you require the ressources. Once upgraded the "old ship" however is gone, so it releases the ressources used in it. It is not an ideal or intuitive system, but you usually don't have the double the ressources invested.