I've never had a track simply not load, but a few on here (including myself) have noticed that track parameters do not get exported (such as hot cues) from time to time, requiring a re-export. As a result, I've habituated the practice of exporting a playlist twice. Now, I've done this over a two releases because there's been nothing in the release notes specifically addressing discovery or resolution of the issue.
There's another reason you might consider nuking the media when you export: Previous sets you exported will have their track's cue points, loops and hot cues reset to whatever your latest export has, so if you (like me) like to visit portions of previous mixes and expect to have your performance settings there...you're screwed. I 'fixed' this by writing a script that makes each playlist use softlinks to files in a unique directory for that playlist. The downside is, if I use track "x" in three playlists, on the media it will be there physically three times. Media these days are huge, so memory consumption is not as important as it was a few years ago. The benefit to me is that set will be there and never change unless I edit it directly, like having a virtual wallet of CDs from back in the day...