This is a little late, but just to let you all know that I found a way around it, so that anyone with the same problem can try it.
Basically I had a lot of 1080i footage mixed in, some of it digitized as very long shots (it was a 15 minute video to show the work done by the local governor in his 5 years in office), so it wasn’t very practical to convert all to ntsc and then edit it again in the time I had left.
However, I found out a simmilar result can be achieved by creating a new sequence, placing the video on that sequence with the shift fields filter set to +1, and no speed change (the flickering showed up when the footage was slown down, I just copy-paste, remove speed and then moved the in and out points a little bit), render it, then go back to the original sequence and replace the 1080i footage with the sequence, and apply the speed change to the sequence. After that, no more flickering.