The 'FIX ME(3)', message comes from the interlaced checked and it's probably thrown since the input file doesn't exist any more. 
Trying to make heads and tails out of what you wrote:
1. you encode a bunch of files
2. you delete the sources
3. then you do something to get Hybrid to run into the problem,..
-> I'm not sure what you do once you deleted the files to trigger the problem
Can you describe a bit more in detail what you do?
Do you trigger the job generation?
Ahh,.. I think problem might be that you not only deleted the file, but also the folder the source was in. (Error will occur once per file inside the queue where you did that, shouldn't look more than that,..)
Cu Selur
Ps.: btw. you might want to update your Hybrid version,..
Trying to make heads and tails out of what you wrote:
1. you encode a bunch of files
2. you delete the sources
3. then you do something to get Hybrid to run into the problem,..
-> I'm not sure what you do once you deleted the files to trigger the problem
Can you describe a bit more in detail what you do?
Do you trigger the job generation?
Ahh,.. I think problem might be that you not only deleted the file, but also the folder the source was in. (Error will occur once per file inside the queue where you did that, shouldn't look more than that,..)
Cu Selur
Ps.: btw. you might want to update your Hybrid version,..