marquis6461

darkly
Are you using Sonarr with PLEX?
If you are,  Go into Sonarr and assign a Recycling Bin in Settings (Advanced Settings Shown) At the bottom.
I had that problem also.  Was confused and thought the same thing. Sometimes Sonarr was bad for that by replacing a good file with a bad one.
If not, I have used Cloud with DrivePool and missed a setting and had my files uploaded to the Cloud.  When I disconnected, I was panicking when Sonarr and Plex found holes showing the file unavailable.  It was because Drivepool was set wrong.
You have to ensure in the Balancing area that the Clouddrive will only store Duplicated files.  You must (MUST) uncheck the Unduplicated block for the cloud drive if you want Sonarr and Plex to behave....

Its a little late in the game but here goes.
 
The biggest task will be allowing your drives to Balance with the Proper File Settings.  For Example Mine.
 
My system is set up according to the Alphabet  Sweet and Simple.
 
Drive Pool 1 is set to T: and Labeled as TV Series - subfolders # thru Z
This allow Sonarr to run and update TV Series.  All active Shows are set to use Season Folders with Format for Shows as Covert Affairs - 01X01-02 - Pilot.
When the Series has ended and all episodes are viewed.  The Show is marked as UNMonitored.  Then it is optimized for TV using the settings in PLEX.
If the file is not on the active viewing, it is Zipped in a fashion that Windows 7 can access it .  It is read only locked  The file will look like Covert Affairs (Complete).
DrivePool can be instructed to Store That Completed file on a particular disk using the plugin 
When you are ready, You can shut the computer down remove the drive, and start it back up
When DrivePool shows its missing.  Remove it.
If the Drivepool has completely Arranged the drive right, you will be able to move the files from under the PoolPart.  The Files will be available most ways possible.  Place a ! in front of the PooPart Entry and it will not join a Pool Partition until your remove the ! from the file.
 
Keep your 10 TB for updates, move them when they are finished.  A Great Bat files checks mine to ensure it is ready and the file is moved to the drive that will keep the copy. 

I find if I remeasure after I move then the system updates.  I also make sure my rules apply to the drive in question.  If I move a file off of the drive that does not have a rule for that folder.  the system catches me on it and moves it according to the rule..
 
As you said Chris.  It seems simple but even the admins can complicate it to the point the system gets mad.
 
Once a month I rotate a drive thru my Pool to ensure my data is not lost using your system.  I love it because it works.  No fuss no muss.
I have created a DP of 30TB Gross with 22.1TB used.  My largest drive is 4TB USB.  All I do is plug the cleaned drive into the system.  Tell DP to use it and assign the same Rules to the New drive as the one I want to swap out.  Your system starts the migration keeping permission active and when it finishes, I disconnect the old drive and move on.
 
The only problem I have is not software related.  My Drobo goes offline for a moment.  The USB dissconnects, DP sees that.  Waits then remeasures as soon as it comes online again.  Can't take it down until I get a new replacement but It works.  As I said.  DP is there working better than a person could want.