I don't know what might work to get a successful encode of the sequence that contains the nest. But here are two possible solutions.
- Double-click the nested sequence to open it in its own Timeline panel. Export that to a lossless or very high quality codec. Round-trip the resulting file into Premiere and swap it into your main sequence in place of the nest.
- Basically un-nest the sequence by using the "KEM Roll" feature to replace the nested sequence with the individual clips that comprise the nest. [If you're not familiar with it, the KEM Roll feature is controlled by the button in the upper left corner of the Timeline panel, the tooltip for which is "Insert or overwrite sequences as nests or individual clips."] Of course, this approach would put you back where you started when you resorted to the nest, needing to figure out an alternative approach to make the quick alteration you refer to. If you explain the nature of that alteration, perhaps someone will have a suggestion.
I'm curious whether the nested sequence itself contains any nested sequence. I've run into a couple of cases where multiple layers of nesting caused encoding to fail. If that's not the case, then this would be the first case I recall where a single level of nesting broke export.