It depends on what version of Thunder you are running. We had an old version of Thunder (pre MXF). Our standard work flow was to import DV files (Pinnacle codec). If necessary we could import HD files – 1920 x 1080, Quictime, animation codec, 29.97 fps. On import it would convert the file to SD (our system was SD only). I recall having to tweak the import settings, however it’s been so long I don’t remember which settings were adjusted.
If you have the newer MXF based Thunder with HD enabled you have a couple of options. Try to find a copy of Thunder Browse, this will allow you to transcode the files into a Thunder friendly format. You’ll need to install it on a PC if you a PC available (doesn’t run on Mac OS). Or you can try to dig up the old Avid DNxHD codecs (v1.8) and then convert the files to DNxHD using TMPGenc, AE or another suitable app. You might find the legacy codecs on Avid’s site.
Hopefully one of these options will work ouf for you. Thunder is either already EOL or well on it’s way. Good luck.