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I think your confusing cut and paste with dynamic link. Import the AE comp into premiere, then drag the AE project file into your timeline don't copy and paste the clips. Dynamic link only works by replacing your clips with the AE project. No more copy and pasting and no more being able to edit multiple clips in Premiere once you do dynamic link.
Screw dynamic link unless your using it only a few times in your project because you need to lock your cut.
Open AE - import - premiere pro project then whatever you have to do.
I know this isn't what you want to hear but it's the best way around your problems.
Thanks for the help John, your method seems to be working quite well, just do all the effects needed and import bck into Pr.
Although, my cross disolves dont seem to work when I re-import the sequence from AE into Pr.
I end up making a slice in the time line, putting the clip onto another video track and overlapping slightly to make the cross disolve work.....dip to black and additive disolve work just fine.
Only a small problem with an easy enough work around though!