Interesting Q! Generally the answer would be No as the going from the original file via the decoder & renderer during playback would result in the best quality, and these days the decoders & renderers should have both broad enough format support and be quick enough. You "may" consider pre-transcoding files if you have:
- Compatibility Issues: eg I transcoded all my DV-AVI files to AVC in M2TS containers as I found support for original DV-AVI was becoming spotty
- Performance Issues: as in your case if your HW can not decode & render in real time you may want to re-encode but in general you would be better to just buy a better HW (eg GPU for madVR).
While there would be 2nd generational loss, as you would be decoding --> rendering --> encoding in most cases you will not notice any loss. As an experiment, try using MC's Video conversion to make a stacked file and see you can notice any issues.
Thanks
Nathan