Excellent. I don't understand how Encore could ask you if you wanted to reimport changed sequences if it was not reverting to original. I now assume that Encore does not address the possibility that you might have multiple sequences on one timeline when it does this process, and does not revert all (or any?) and produced the gaps.
So, in any event, your multiple DL sequences on one timeline worked, once you reverted and adjusted. The alternative to what you did would be to answer "no" to reimporting, then revert (which would pull in the newer version). If it was not actual changes that contributed to the gaps, that might avoid them. But I suspect you would still have to adjust the sequences on the original timeline.