When you replace a clip from PrPro timeline with an AE composition, After Effects creates a brand new composition and imports the source footage in the project as well. Since both PrPro and AE work in non-destructive way, the source footage imported into AE project is the same one you utilise in PrPro project. However, within that newly created comp it should have correct In and Out point. E.g.:
Sorry that just does not seem to work. The highlighted section is not that same. and what if the clip is long? You have to scroll through all that footage to fine the correct in and out points with no sound. I still don't understand. Please more help is needed
Sorry, but something is definitely wrong with your workflow but not with the above.
When you select a clip or a group of clips in PrPro timeline and then choose 'Replace With After Effects Composition', AE creates and automatically opens a brand new composition, in which number of layers and their In and Out points correspond to a number of clips replaced with AE composition and their In and Out points in the PrPro Timeline accordingly (i.e. layers in that AE composition are appropriately trimmed and distributed in time).
See another one image, if you didn't notice that in the previous one the layer was trimmed:
So, the question is, what do you do to achieve what you see in AE, since you shouldn't do any extra steps to get correct result, 'cos AE opens that newly created composition automatically? Do you jump back to AE Project pan in an attempt to create a composition out of imported assets once again?