DT Indexed PDFs in Dropbox Folder (Linked via in Zotero/Zotfile) Delete When Annotated

So, here is my setup. I link pdfs in Zotero by using Zotfile. The pdfs are stored in a Dropbox folder and linked to their Zotero citation. When I open these pdfs and annotate them, I use PDF Expert (on Mac and iPad). The whole system works to integrate citations and annotate pdfs. I have this same folder indexed with DevonThink.

When I link pdfs through Zotero/Zotfile they sync well with the indexed Database in DT.

However, when I annotate a pdf with PDF Expert on my iPad and sync the annotations the pdf gets deleted from my Dropbox folder. I am fairly confident that something in DT is deleting the pdf. When DT is closed, the whole process works: linked file via Zotero/Zotfile syncs to Dropbox folder and annotated pdfs update and stay linked. However, when I open DT and it does its indexing, the updated/annotated pdf gets deleted.

Any help on this would be greatly appreciated.

Unless you’re using a smart rule that moves items to the database’s Trash, DEVONthink will not delete items without your intervention.

Is PDF Expert saving the annotated PDFs to a different location in Dropbox?

Thanks for your reply.

I don’t think I have any smart rules set up.

When I annotate the pdf with PDF Expert on my devices (Mac, iPad, and iPhone) it updates the same pdf file at the same location in the Dropbox folder. This Dropbox folder is where the Zotero-linked files are stored. This same folder is indexed in DT. The pdf file also seems to sync well in DT when it is first put in the Dropbox folder by Zotero. The sync of annotated PDFs also seems to work well when DT is closed.

However, when DT is open and actively indexing this same folder after the pdf is annotated on my iPad the pdf on Dropbox gets deleted in Dropbox. Oddly, this only seems to happen when DT is open and the pdf is annotated. Any ideas?

Again, thanks for your assistance.

You’re welcome.
When it happens, selected the indexed group in DEVONthink and choose File > Update Indexed Items. Does the PDF reappear?