My two cents here are, to simplify your workflow (DT: macOS DEVONthink, DTTG iOS version):
- Use DT/DTTG in as many tasks as you can accomplish.
- Don’t use PDF Expert in iOS, and directly annotate inside DTTG. The annotations tools are good for normal annotations.
- Don’t annotate anything in DT if you don’t want the PDF to go corrupt (to clarify, I mean in macOS only). It is not a DT issue but macOS itself, as the PDF framework is very buggy, and each new macOS version goes buggier. Don’t annotate as well with integrated macOS Preview app. Use PDF Expert or another tool in macOS that doesn’t use the integrated PDF Framework.
- In DT, extract the annotations from DT itself. It will generate the file and my next step is simply store it in other database for further reference and/or searching, but you can export or index to another platform.
- Annotation exportation from inside DT can be (more or less) automated: Stream annotations from your PDF reading sessions with DEVONthink - DEVONthink / Automation - DEVONtechnologies Community
- If you scrap from web, you can automate and make some beautiful scraps in PDF: DEVONsave v3 (fulcra.design) (There are some discussions inside the forum about this, but no one directly presenting the last compatible version, then I put the original outside link).