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zan5hin - maybe you could use one of the file system monitors (I use one called Watch4Folder) to detect the arrival of new PDF's in your calibre library. When when it detects a new PDF it could copy it to the \iCloudDrive\GoodReader\Books folder.
You will need to consider the possibility of non-unique file names.
Maybe the copy could be a script that extracts the book number from the calibre book folder - i.e. the number in parentheses at the end of the book folder name - which it would pre/app-end to the pdf file name in the iCloud folder.
Might need to be a two step process - I don't like the idea of renaming a file whilst its being synched to the cloud, assuming it's even possible. Copy to staging folder, pre/app-end book number to name, move to \iCloudDrive\GoodReader\Books. If the staging folder is on same drive as the iCloud folder the move will be fast.
To get the Annotated PDFs back into calibre - maybe you could monitor the \iCloudDrive\GoodReader\Books for updates and copy the files to the calibre Autoadd folder see
Preferences->Add Books->Automatic Adding. It should be possible to set it up to replace the existing PDFs.
You could run the iCloud syncing service continuously. You won't run up against
this issue (
← click), because you would NOT be synching the calibre library itself.
BR