Batch transcoding for Blu-ray

Question

Hello,
We have many short ~2 minute files with long filenames (so they can cleanly be used to form the chapter descriptions for the disc) organized into folders and, as mentioned in another thread, we are having difficulties preparing these files in advance for Blu-ray processing for Encore so they do not need to be transcoded when we select 4-5 to author a Blu-ray with.  I tried to get around this by creating a massive project with all 500 of our files, using Encore CS6 to transcode all of them, then hoped Encore would know it transcoded that same asset in another project when we went to use 5 of those same files in another project.  Unfortunately, not only did Encore not automatically detect that it had already transcoded the file for Blu-ray in another project, but when we went to manually locate the file, we saw that Encore truncated all our filenames to 20 characters in the Transcoded folder, followed by "_sessionA_blahbalhablh.m4v".  Our filenames are not unique to 20 characters, so many filenames with A, B, C, D, etc suffixes were created and we have no way of telling what file is what.  We can't even play the file to check, and we also can't compare the running length as Encore transcodes to elementary streams that can't be played back.  Is there anyway to copy the transcoded asset knowledge from one project to the other so we can make use of the 3 days of compute time we appear to have wasted? 
I've also looked into using Adobe Media Encoder to do this, but I think I'd need to take our files one folder at a time and run the transcode on them so they didn't get jumbled with the other files.  I can't see a way to setup AME so that it handles recursive folders, and I also can't see a way of working with AME through command-line automation so that it can whir away and process one folder of 5-10 files at a time.  All I can see is a way for it to turn out a similar output to our failure with getting Encore to transcode the files.
Any ideas on how we can batch-transcode for Blu-ray ahead of time instead of wait for Encore to transcode for every disc we build?

Answer 1

Encore is not long filename friendly, and will cause problems if you exceed an 80 character filename (Including spaces). Odd characters and in some cases excessive path depth can also be issues. The Encore authorcore (sonic based) is old, and just not modern filename friendly.
So I'd rethink the long filenames generally.
Ask your AME question in the AME forum. I do not know whether there is a good option for you or not.
hoped Encore would know it transcoded that same asset in another project when we went to use 5 of those same files in another project.
Encore creates a folder structure for the project, and under the sources/transcodes/ folders, a folder for each asset that is transcoded. As soon as you create a new project, all that is gone, and with it encore's memory for it. You can import those files as assets, but I assume your point is that you can't tell what is what.
We can't even play the file to check, and we also can't compare the running length as Encore transcodes to elementary streams that can't be played back.
The elementary stream is an m2v. You can play these (e.g. with vlc player). But all that would be cumbersome.
Still thinking about this...