When you nest a project in another project, there is no link to the original project. Dynamic Link will link multiple AE comps, but it will not link AE project files.
I keep my workflows organized by file naming conventions that start with job numbers and are organized the way I was taught when I started editing movies shot on film in the 1970s. It's the same basic system studios have used in feature film productions since the 1920s.
I also make extensive use of MOGRTs and Animation Presets. I just checked my Custom AE presets folder. I have 313 presets there for everything to multiple-layer animated graphics with names like 2103CM_MstrSubTitle_txt, 2103CM_MstrSubTitle_subtxt, 2103CM_MstrSubTitle_bg. This set of animation presets will generate a lower-third graphic for my client, CM, that fits any sized comp because of the included expressions. All it takes is an empty comp of the desired size and three double clicks in the Effects and Presets panel, starting with the bg (background) preset and moving up. If the client needs a change, I can then modify that master project, replace the modified Animation Presets, and generate a new MOGRT that I would name 2525CM_MstrSubTitle, reflecting today's job number (2025CM) and the graphic (2025CM_MstrSubTitle.MOGRT) I created for my client. I then share the new master MOGRT with the client so everything matches. The number of custom animation presets goes up and down every year as I clean up, organize, and archive my files. I can find enough information in my archives to find design guidelines, samples, and notes that will allow me to recreate projects that match the designs I created in 1994 when I started using After Effects and archiving my work on a computer.
This is the most efficient workflow I can think of until AEP project files maintain a link to any imported projects. It simplifies billing because of the Job Number and time tracking by job number and provides clients with a very simple way to manage their in-house productions and match any changes to their Brand Standards.
I hope this helps.
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