I’ve been dealing with this problem on a 30 minute long project with tons of multi-cam, 6-channel audio nested sequences. I was surprised to find that my OMF’s opened perfectly in Protools if I selected the “encapsulate audio” option with short handles (to keep the OMF file size sub 2GB). Based on this, my suggested work around would be – use timecode to divvy up your sequences into sections that fit below the 2GB limit – and then stitch them back together in Protools.
Far from ideal, but faster than conforming un-nested footage back to the nested edits.