From the way your talking i take it yours is the w209 CLK version. Its easy to reset the rear headrests which deploy & act as a roll bar once they come up by carrying out the procedure you've already previously done. It makes no odds whether the roof is up or down except that with the roof up & closed you have to climb into the back of the car & be a bit more forceful. When i reset the headrests i use a long 6mm allen key. Make sure the keys out of the ignition for safety reasons & then on each rear headrest you need to feed the allen key down the righthand side of the headrest roughly in the middle & feel for a spring loaded resistance. Press the allen key down hard with one hand & then at the same time push down hard on the head rest until its fully down & then realease the allen key. The head rest should then be locked down & you can move to the other side & repeat the process. Once done the roof should all work ok again.
The only thing i'll say is that if your claiming through your insurance for rear end damage it may pay you to leave alone until its been assessed or repaired as its all evidence for your claim if you see what i mean. At the end of the day though if your finding it hard to drive your car because you have no rearward vision then get them reset but speak to your insurance company first just to advise them of the situation.
Hope i've been of some help & good luck with your repairs.