In Iowa, the Big Brown Bat and Little Brown Bat, the ones most likely to enter homes, are not protected in structures occupied by humans. You can do whatever you want with them in your house. Complete Wildlife Control uses humane methods for bat control and this information is for homeowner use only.
This is the Iowa code from 2021:481A.42:
Nongame protected – exclusion. Protected nongame species include wild fish, wild birds, wild bats, wild reptiles, and wild amphibians, an egg, a nest, a dead body or part of a dead body, and a product made from part of a body of a wild fish, wild bird, wild bat , wild reptile, or wild amphibian. However, nongame does not include game, fish that may be taken pursuant to regulations established under the Code or departmental rule, fur-bearing animals, turtles, or frogs, as defined in this chapter. The commission shall designate by rule those species of nongame which by their abundance or habits are declared a nuisance, and these species shall not be protected. Rules adopted shall include, but are not limited to, a provision that states that any bat , except for the Indiana bat , which is found within a building that is occupied by human beings is not a protected nongame species.[S13, §2563-q C24, 27, 31, §1776 C39, §1794.005 C46, 50, 54, 58, 62, 66, 71, 73, 75, 77, 79, 81, §109.42]83 Acts, ch 168, §6 92 Acts, ch 1107, §1C93, §481A.42
Complete Wildlife Control uses humane methods for bat control and this is for homeowner use only. Bats are only federally protected if they are on the endangered species list, which in Iowa, only the Indiana bat and Northern Long-Eared bat are. Complete Wildlife Control has never found an Indiana bat or a Northern Long-Eared bat inside a house.
If another company has scared you into believing bats are federally protected, ask them to prove it.