Not normally! Trifluoroacetic acid (TFA) will not alter the column chemistry of Cogent TYPE-C™ columns.
If you have a method that uses formic acid for example and then try a TFA method on the same column, you can go back to the formic acid method and obtain the same retention behavior as before.
Use of TFA does have other considerations, such as with LCMS. In this case you should avoid use of TFA if possible or use very low amounts (0.05%) because of the Mass Spectrometer issues.