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, 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 LC-MS. In this case you should avoid use of TFA if possible or use very low amounts (0.005%) because of the Mass Spectrometer issues.