The good news for PC players is you can actually use a save editor on the ME1 save to edit the flag for Conrad encounter. Basically, it ticks both paragon and renegade box on how you dealt with him, so you just have to untick one box and save the file again. Once you fix it after it is set, it is done for the rest of the save files, or you can just modify the very last save that imports before importing.
Consoles....sorry, don't know of anything that can be done. I know old editor worked on Xbox saves, but I don't think it does on MELE save editor...nexus mods has the editor if someone wants to look for it.
