Vibrational relaxation and isomerization of internally excited deuterated formyl and isoformyl cations has been investigated on the time scale of 2 ms to 12 s using the nearly interaction-free environment of an ion storage ring. De-excitation of the v(2) bending modes of DCO+ and DOC+ due to spontaneous radiative transitions was observed as a function of the storage time by measuring their foil-induced Coulomb explosion using three-dimensional coincident fragment imaging. No isomerization of low-lying vibrational levels of DOC+ ions was observed on the time scales considered. By comparing the Coulomb explosion data to molecular bond angle distributions obtained from vibrational wave function calculations, the time evolution of the mean v(2) population is deduced for both isomers. The stored DOC+ ions are found to thermalize with the 300 K black-body radiation, while relaxation of the DCO+ bending vibrations was found to require considerably longer times, in agreement with a predicted very small transition moment of the v(2)=1 level.