In the UK, a number of TV series (mainly comedy) have 2 broadcasts - the original version and then the extended version. Rather than have 2 separate folder structures (with information sourced from the TVDB) I have a single folder structure for each show.
When for example QI is broadcast, I download the episode (as a UK TV license payer I'm allowed to!) and publish it to Plex. My tablet is setup to synchronise unwatched items of the series for me to watch at lunchtime at work.
The next day when the extended version is broadcast, I download this new version (44 minutes as opposed to 28 minutes typically) and overwrite the existing file in the QI folder. I then manually analyse the file in Plex to update the fact that it is now 44 minutes long as opposed to 28 minutes.
If I synchronise my tablet after this, the change in the programme length is not detected so that Plex offline reports an episode of 44 minutes but plays the previously synced 28 minute episode.
Please update the sync to not only look at the watched status, but to also look at the length and quality of the server episode and download/replace as appropriate!