What version of Premiere are you using?
When you send a Premiere Sequence to Media Encoder via the "Queue"
option, Premiere saves a copy of the Premiere Project here (Win):
Media Encoder uses this copy as the reference while encoding,
so you are able to continue to work in Premiere without problems.
However, Media Encoder (and its 'Temp' Premiere Project) will
continue to look to the original Dynamically Linked Ae files for encoding.
If you want to continue working on an Ae comp while an encode
in in progress in Media Encoder, you should save an incremental copy
of your Ae file (Ctrl+Alt+Shift+S) before you make any changes.
If you do this, it will not interfere with the ongoing encoding.
Thank you for the helpful response.
I am using Premiere Pro CC on a Mac. I will also be using a Windows machine in the future.