So i have been working on the Avarice of the Scruuge seasonal mission which produces 4 Scruuge Behemoths to battle, 2 of which were on my BT tab. I was working on another mission and used the tactical remodulation ability and it wiped these specials too. Is this right, if theyre limited in number and part of a mission shouldnt they sit still? Are they gone forever with no way to redo the mission to get them?

Yep, it's right.

Tac Remod will get rid of any and all unshared NPC's on your battle tab.

Is it something people agree about, nope, but c'est la vie.

Send Dan an in-game report and he'll probably respawn them for you, or just chuck the modules into your cargo for ya.

Description is pretty clear about it:

Tactical Re-modulation
Removes all non-player enemies in your battle tab, allowing new random enemies to appear.
Does not remove enemies that have already been shared with your legion.
No rewards are given for enemies dismissed this way.