For example let's say you have a nested sequence with one clip inside fully used. In the parent sequence, you only select a part of the nested sequence.

Now you launch PlumePack from the parent Sequence and choose the options to optimize the disk space. In that case if you choose the "Remove Unused Elements in Nested Sequence" (or "Remove Unused Elements in Muticam Sequence") AND trim from the parent sequence (chosen in the PlumePack option), the clip in the Nested Sequence will be trimmed based on the parent sequence use. That's why you could end up with a clip in the nested sequence with diagonal danger lines in the timeline, but actually they should be reference to a part NOT used in the parent sequence.