Not sure how to clean more than once as once cleaned, cleaned (gone). 
Reduce the number of variables. I’d suggest first get Bonjour working, say with one database, then add more as success is achieved. It’s the simplest, quickest, and most reliable. Does not involve having any files in any sync locations or any cleaning required. Maybe a fresh start with DEVONthink to Go reinstalled on your iOS device(s) will allow that fresh start. Follow instructions from the DEVONthink Manual, supplemented by Bonjour Simplified.
As is clearly documented and mentioned here, Apple’s iCloud unreliable for some (many?). And from reports here and on other app/developer forums it’s getting worse over time, so I guess you are experiencing that. Apple provides no “knobs” to turn to enable people to kick it into action or debug issues.