Older Carbon Bike Safety I have an older Trek 2100 that has carbon fiber tubes with aluminum stays (The frame is used early 90's 2100/2150/2200/2300 road bikes)

After a recent accident with a car (going down hill, guy pulls into the road from a driveway  and just... stops, so I bounce off his door) I took my bike to a shop to check for frame cracks, which they didn't find thankfully.

They did point out though that in the lower frame joint (by the front derailleur) the carbon tubes are separating from the aluminum joint. This is apparently unrelated to the accident and something that naturally happens as the epoxy ages and the bike is regularly used.

How dangerous is this? How likely is it to catastrophically separate outside of an accident type situation (i.e. just riding around)? And is it possible to rebuild the frame with fresh epoxy (I have access to a machine shop and some industrial grade epoxy)?

I love downtube shifters too much to just toss it away :D
As far as I know carbon is most prone to catastrophic failure of all frame materials. Depending on the type of separation you see it could be a bit dangerous to keep on using your bike as is. The catastrophic failure occurs because the epoxy becomes brittle over time. A new layer will probably extend the life of your frame just by protecting the original epoxy from the elements. However, it will also hide the progress of the degradation of the material underneath, so you won't be able to monitor the extent of the degradation. I'm not sure you could repair your frame to the extent that the new layers will be strong enough to replace the old ones.

But I'm not an expert, so I could be very wrong. Maybe your best bet is to send these guys a picture of the damage and ask them for their professional opinion.