Truhe:
If I empty the store, sync with one machine, then connect another machine to the same store, will this machine recognize that it already has about 95% of the store entries or will it up/download everything and create duplicates in its own database and the store (and therefore in all other clients as well)?
Yes. Each record has a UUID that is, mathematically, globally unique and used to match the records in the remote store/machine to your local machine. DEVONthink won’t transfer anything for which you already have a copy.
We now have encryption, which is fine. But we don’t know how the encryption works. There’s one comment for the blog post which mentions that there is a unique key for each database, but we don’t know when and how this key gets generated, what we should do if the decryptions breaks and how other DTPOses handle the whole encryption and decryption, because they use other local databases which talk to the same sync store to, well, sync.
This thread has some of the answers you seek.
DTPO decides for itself whether it encrypts or not. If you don’t want encryption, you can’t disable it, which means that we have to trust DT, which we can’t, because of (1).
Ask and ye shall receive. There are no secrets, only questions that haven’t been asked.