Do you mean offense position guardian ? like number 13 in the picture ?

you cannot loose it because he doesn t leave your city ( just go to persian and back ), but you can / might have used it to upgrade another guardian ?

That the only logical explanation.

you can get  more guardians with emeralds ( also rewards from warlords fights ), and more emeralds by leveling  your guardians / participate to xp guardian tournements

make sure you lock all the guardians you want to keep, that way you cant use them to upgrade other guardian by accident

to do this, select the guardian you want to lock so its tats are shown, click on the lock symbol on top right and then a lock symbol will appear on the picture of the guardian