As mentioned before, Greg is the local (pun intended?) authority on indexing here (usually, after I have run into issues in the past, I’ve come across a post by Greg or get a response that sorts me out), and if I understand him correctly this time, indexing a folder on your computer that is also syncing with Dropbox (for example) is no problem.
My experience has been the same—no issues at all with mixing indexing and data synced to Dropbox.
There are some interesting conundrums you can create for yourself this way, though. For example, let’s say that two databases index the same file, but you delete the file in one database. That’s OK, surprisingly, as long as you have both databases open at the same time (I haven’t tried it yet with one closed and one open, but that seems like a bad idea).
But, let’s say that you fiddle with a file using another app on iOS (maybe a text editor synced with a file in Dropbox), then mess around with the file in DTGO on iOS (remember, it is indexed, but on the computer), and then mess around with the file on OSX with DT. I’ve generally found this to be a stupid thing to do, with unexpected results, (apparently) depending on settings dealing with sync conflicts and the quality of the apps that get enmeshed in this sync nightmare (lots of sync conflicts in the text editor I used to use on iOS before DT got markdown support).
How about a local folder not synced to Dropbox, indexed into a database in DT, synced through Dropbox, and then opened on another computer? Interestingly, the indexed folder (which originally only existed on the first computer) is indexed and created on the second computer. Wow. Am I understanding what happened correctly? You are now “indexing” the same folder that exists simultaneously on two different computers that are only synced through the DT app—a kind of double indexing. Obviously, a recipe for trouble if you are not careful (for example, mucking about with the files on one computer while forgetting that DT is syncing them to another one), but also an elegant solution for a user intent on indexing and syncing between two computers (me). Naturally, backups and lots of testing in tiny baby steps is recommended before jumping into a workflow like this.
But, the gist of my message is that indexing can be rather amazing in its ability to accomodate unconventional workflows, and reliable to boot.