Nope, nothing permanent. The character's DNA will just take a while to get ride of the foreign stuff, but get rid of it it will. xD
And yeah, we're giving you a lot of freedom in how they'll be handled, as long as it's reasonable. The mutation can stick around unchanged for a chunk of the time and disappear in a shorter frame or disappear over the entire frame of time - as long as it makes sense and isn't there one day and gone the next or remains unchanged through the entire thing.