When I have two replicants of fileX in two groups, and I delete one group, one version of fileX appears in the trash and one version stays in the undeleted group. Then, when I search for that file, the one in the trash shows up, but not the one still in the database. Is there any way to get the search to exclude the trash by default?
Thanks
Click on the DEVONthink application name in the menubar and choose Empty Trash to flush items to the System Trash.
Items within database Trash remain searchable (this is desirable).
You can select the *database in the Trash in the Sidebar, show the info ( command-shift-i) ,and click on the checkbox to Exclude from>… Search.
*Edited to clarify that you have to select the specific database from Trash in the Sidebar. One cannot select ‘Trash’ and apply the exclusion to all databases.
This is true but we really discourage people being lax in emptying their Trash. It’s not another filing cabinet any more than any other trash can is. 
Valid point, however the OP didn’t ask about proper housekeeping of items in the trash-the OP wants to exclude deleted replicant(s) in the trash from inclusion in a search. That’s a very different question, and I too find what the OP is looking for to have value.
As a FYI, this suggestion only works with deleted instances of replicants. Be it a bug or a feature, a global search will still include documents in the trash where there are no replicants in the database (which is why I find it useful).
To clarify - it doesn’t bother me that the search returns the replicant that is in the trash - it bothers me that is does NOT return the other replicant that is still in the database - I ONLY see the replicant in the trash, even though another is still in the database. I was hoping that excluding the trash would force the search to show the result that is in the database, but I would really like to see the search prefer to show the replicant that is still in the database if it has to chose only one replicant to show.
Is it possible to have search [i]prefer[/i] to show replicants in the database over one in the trash? Or even to show replicants that happen to be in the trash twice - one for the database version and one for the trash version?