Struggle with my Workflow (Macbook, iPad, DT 3, LiquidText, Papers)

P.S.: LiquidText (LT) has an “Auto-Send” feature → “automatically send annotations on your PDFs back to their source files”. This would help but doesn’t work reliable. Seems that the link between the external file and the LT internal representation gets lost and I found no way to edit the connection again.
DevonThink also has some sync problems with the index files. I have to refresh the folder manually most of the time on my Mac to see the current list of files. And it always takes some time until DTTG reflects the changes visible in DT