Premiere Pro Project Manager does NOT include After Effects files.

Warning: Premiere Pro "Project Manager" does NOT include the After Effects 'dynamic linked composition' files associated with the project when "Collect File and Copy to New Location" resulting in the incomplete and loss of all dynamic linked compositions in the new project destination ( folder or disc drive ) .. I know this also includes Photoshop dynamic links and assume includes Audition audio files as well.

Here's the best way: Personal Responsibility.
Put all of your project files in one file. Stop asking PPro to do it for you. It's simple. This is a no-brainer. If you create a linked comp, create it in the same file as your PPro project and files. When you send it to Encore, create the Encore project in the same folder. Works all the time, every time. When you're sure that you're finished with the project for the forseeable future, move the entire folder off your workstation into storage. Do I move a copy of each asset (video clip, image, audio, etc.) into this folder before I import it to my AE or PPro project? Yes I do. Is it overly time-consuming? Not really. I can fly on my machine. Does it beat not being able to open a project later. Oh yes. Yes it does. I'd say I did 50 projects last year this way. When I occasionally had to move a project folder back to the workstation, I had no problems. Everything worked as it did before I off-loaded it. That's because I take personal responsibility for my projects. It's imporatnat that theyt work, especially if I end up having to hand it off to a third party down the road.
BTW, my workstation is RAID 0. If you are using anything less, you need to upgrade. What I'm trying to tell you is that my system works very well. I have not always done things the right way. I have had my share of frustration. The point is that I learned. Now I'm passing that on to you. I use CS5 on an HP Z800 with a measely 12 gigs of ram and a single i7 quad core and the aforementioned RAID 0 configuration and a hacked Nvidia GTS 450. It works quite well. I'm sure I would do even better with another i7, 12 more gigs of ram and a Quadro 4000, but this is what they give me to use.
Additionally, I'm using CS5 at home on a MUCH older HP xw8200 dual dual Xeons, 12 gigs of ram and software-only MPE. Guess what? It works quite well.

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