If I star a paper in paperpile and then annotate the file in either the starred or alphabetical Google Drive folder with an external application or upload a new version in the version history, will this be synced back to paperpile and across folders?
Yes that works.
If you annotate a PDF in an external application and the file is correctly synced back to Google Drive the changes will be reflected in Paperpile. Paperpile will notice that the file has been changed and will show you the updated version. The file in the starred folder and in the main alphabetical folders are always identical (i.e. they are not copies they are the same file), so that should not cause problems.
The only caveat is that if you use a sync client, like for example inSync on Linux or GoodReader on iPad that do not fully and/or correctly implement the Google Drive API, this will cause trouble. See here and here.
But with generally the workflow you describe should be ok.
I have tried several pdf annotation apps on Android but they all showed that the pdf file is read-only and I need to save the file to a local directory and then manually upload the file. This was a headache for me for a while. Then I found that ES File Eexplorer can connect to gDrive. Once you open the PDF from within ES, it automatically sync the annotations back to gDrive.
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