Erm... That's normal. Once you EXFuse two characters, they will be unavailable until you revert the EXFusion. Which I'm sure you already know.
...Unless you meant something else. I'll have to check your save file.
So... You want Trunks (Super), Kid Trunks, SSR "Hold your fire! This man isn't Black." and Broly (LSS)? Very well.
Can't. Those are special.
I can add them into your team, but then they will be gone once you change your Team Members.
What I can do, is create a team with: Gotenks, Gotenks (SS), Gotenks (SS3), Gogeta and Gogeta SS4.
And a second team with: Yamhan, Pirillin, Natz, Recurter, Gulce.
(Or a team of your choice, then just simply register it. I can even change its name, if you want.)
You need to freeze the 'Have all Characters' code if you want to freely add the Metamoran characters in and out of your Team.
(A code which you do not have.)