A while back I had several issues with clips not trimming properly during the Consolidate and Transcode process. I reached out to Adobe support and was given this fairly comprehensive list of when and why clips will fail. For some reason, this list is not posted publicly anywhere. I've copied it in it's entirely below. I've bolded several line items I feel are fairly important. There are now essential features in Premiere that I skip using (such as the Master Clip Effect layer) since it breaks the archive process.
These issues affect all versions of Premiere, including the current CC2017 version - 11.1.2 (22)
Hopefully this will help some people with project management.
- If any one of the 4 major video parameters (frame size, frame rate, fielding, PAR) do not match or are not supported by Preset/codec, then entire clip will copy.
- If the clip has multiple stereo channels of audio. These can only transcode to QuickTime, all other formats(e.g.: DNxHD) will fail and copy, since the other exporters do not support multi-stereo (QuickTime is the only exporter that currently supports that and only with uncompressed audio)
- Time remapping is not supported. Will copy entire clip without warning.
- There area number of formats/presets that are not supported for transcode (e.g. mostly still formats)
- Merged Clips are not supported.
- Copy of folder structures (e.g.: P2, AVCHD, etc.) is not supported. Depending on format, some files may be left out or other issues.
- Master Clip Effects are not supported, and will be copied without no warning. This includes all the formats that now have source settings as Master Clip Effects (e.g.: R3D, ARRI, etc.)
- Audio only files
- If used in a merged clip. Unused merged clips will also copy.
- Render and Replace files, even if unused
- Clips with dual mono (2 mono) will copy, although they may also transcode (this is a known bug), but the project will always link to the copied clip and not the transcoded clip (using up even more space)
- Clips with single mono audio will also fail to transcode.
- Modify > Audio Channel changes may also result in failure to transcode.