Other data on an external HD used for Time Machine back-up

I am turning on FileVault on 10.6.8 and, becuase of the space requirements, I need to move some data on to an external HD; this data will no longer be on my MacBook. I use this same external HD for Time Machine back-ups. If Time Machine is doing a back-up onto the external HD and it finds additional data that is not on the MacBook, will that additional data be deleted as it isn't consistent with the data on the MacBook?