...the media was sitting in my computer for about 2 months untouched. Today when I came back to start again a lot of my media had went offline
That is not normal behavior.
Either something changed, or you have a configuration problem.
These audio clip references will be deleted, and cannot be undone. Do you want to continue?......
It's never a good idea to click 'ok' on a message like that
unless you know exactly what you are doing.
I would suggest trying to recover the Project from an Auto-Save.
If your Auto-Saves do not work, you can check in the following
folder for old Project files (pc):
C:\Users\< username >\AppData\Local\Temp
When you queue Sequences from the Project to Media Encoder,
Media Encoder will leave a copy of the Project in this folder.
I was able to work around the problem by moving the media to another location (outside of the original route folder) and then replacing the footage in my project bin with that clip. The audio came back to the clip in the source monitor but not in the timeline. I simply just took the in/out points from clip on timeline and found the audio from the source file. Takes a couple extra steps and I know doesn't fix my intial problem...but works.
Whew! That was close.