Hi Viktor, I presume that your molecule is a base. By taking spectra in CF3CO2D it will be protonated. This will result in 13C signal shift which could lead to:
split of overlapping signals
tautomer's or loss of symmetry which then results in "new" peaks appearing in your 13C spectra
Check the total number of carbons and try to run HSQC and HMBC to get a clearer picture if you are still in doubt
Dear Viktor, if you see proton signals in DMSO-d6 which then disappear in CF3CO2D, most likely they are exchangeable protons and get replaced by solvent deuterium.