It’s a good idea to make sure all clips are optimally synced in PluralEyes before you export the results. After the automatic sync finishes, you can perform a few quick checks in PluralEyes. If the clips didn’t sync optimally, you can troubleshoot the sync results.
Alternatively, at any time you can export the timeline to work with your footage in an NLE. Even if some clips did not sync optimally in PluralEyes, you can sync them manually later in your NLE. However, it is generally more efficient to use the PluralEyes features that help you troubleshoot unsynced and incorrectly synced clips. This is particularly useful if you plan to export the timeline as video files or audio files.

Occasionally, PluralEyes 3.5 marks a clip as being synced or unsynced, when it's really the opposite. You must change the status of this clip before you can fix the incorrect sync.
To change the sync status:
An “unsynced clip” is a clip for which a matching clip could exist, but for which no match has been found. PluralEyes thinks these clips should go somewhere but it's not sure exactly where — so it marks them red, as unsynced.
Red clips could be:
There are other techniques for moving unsynced clips into place in Touching Up Sync Results.
In some projects, clips can be synchronized so the timing of each clip is defined in relation to all other clips in the project. A good example is a live event in which at least one audio recorder is on for the whole event.
In other projects, the timing of each clip can be determined only in relationship to one or multiple clips that were shot at the same time. Each cluster of clips that are synced with each other is known as a “sync group”.
A good example for using a sync group is a narrative film project. Let’s say your movie crew shoots a scene, then turns off all the cameras and audio recorders while they prepare for the next scene, and then shoots another scene. The clips from each scene form a sync group.
Locked together. In a sync group, the clips are automatically locked together. If you move one clip in the group, the other clips also move with it.
Sync groups should not overlap. Occasionally, the automatic syncing process puts clips into two sync groups, when they all should have gone into the same sync group. PluralEyes alerts you to situations in which this might be the case. A red stripe is shown across some of the clips in the sync group, indicating that the sync groups might overlap with each other.

Sync groups should overlap. Sometimes you might feel that two sync groups ought to overlap. For instance, if at least one clip in one sync group should have been synced with at least one clip in the other sync group. In this situation, you can merge the two groups by using touchup sync methods on any pair of clips that should be synced together.