I have discovered a reason why I’m finding my PDFs no longer editable after highlighting them. This seems to be a common issue here, here, etc. to which the workaround is to enable the ForceEditablePDFs hidden preference. However, this may be the first step towards possibly solving the issue and avoiding the setbacks incurred enabling this hidden preference.
Once a PDF is edited (highlighted, annotated, shapes added, etc.) upon putting my Mac to sleep, I am finding that when I wake my Mac, the document becomes read-only. Specifically to reproduce this:
- Import new PDF item
- Open in viewer/editor
- Close mac laptop or put screen to sleep
- Wake Mac and flip from new untouched PDF to new one and back. New one still editable.
- Now, create an annotation/highlight/etc on this new PDF
- Put Mac to sleep again
- Wake again and flip back and forth. Now, PDF is uneditable.
Please someone confirm this so I don’t feel like I’m crazy 
MacOS 13.4 - Apple M2 Pro
DevonThink 3.9.1 - Brand new database
Welcome @Servinjesus1
This has already been reported multiple times on the forums.
https://discourse.devontechnologies.com/search?q=pdf%20issue%20order%3Alatest
That being said…
Is there a crossed-pencil icon on the right of the Navigation bar above the view.edit pane? If so, the property icon shows it is read-only, most commonly due to fonts that aren’t compatible with Apple’s PDFKit. In such cases, annotating a problematic PDF like that can lead to the entire text layer being corrupted. Therefore, DEVONthink detects it as a potential problem and sets it to read-only for safety.
With problematic documents, I would suggest trying Data > Convert > To PDF (Paginated) first. If that doesn’t work, you can open the document in an external PDF application like Preview, and annotate there.
Development also suggests this: Select the Help > DEVONthink 3 Help > Documentation > Appendix > Hidden Preferences. On macOS Monterey or later, Control-click the On link for ForceEditablePDFs. Then paste the URL into the address bar in Safari, okaying opening DEVONthink. This should minimize false positives when detecting potentially problematic documents.
I have seen the other posts but not one that details the fact that files themselves are being corrupted as a result of DevonThink. In fact, I believe I have found the culprit for my specific issue, or at least can reproduce the problem. See my updated main post.