Final Cut X reading from 2 different drives

I am currently sitting at my work desk and our workflow is set up that we have all our projects on the scratch disk to work from, and the back up drive updates every night backing up the computer and hard drive. Because of this, FCPX is reading the events from the main drive and the events from the back up. Every time i open final cut the events are on a different drive.  So the first time I saw this i tried to get all the events back onto the main drive, thus duplicating the events.  Then i noticed that all the duplicated events went onto the backup drive and off the projects drive, i restarted FCPX and it reversed again! Mind you, the events and projects are still in tact on the drives in finder but I don't know for certain that I am working from an event on the actual scratch disk or from the backup drive which could create problems. 
I understand that FCPX has it's own heirarchy within the software and i havent moved any files around within finder only from within fcpx
these 2 pictures were taken 2 minutes from each other to show what happens.
I am also getting this prompt every time I start FCPX
I'm scared to delete any of the events becuase at this point I have worked on diferent projcts and i'm not sure which event those projcts were pulling from. 
I want to know a couple things
1.) why is this happening and how do i stop it?
2.) in the future how do i stop FCPX from reading from the backup drive?
3.) If I do decide to delete the duplicates and in the event a projct i was working on was pulling from that particular duplicate, will it be easy to re-link the media I used?
Thanks in advance for the responses. this has become very frustrating.
Steve

Thanks so much for this help.  It definitely gave me a starting point and a workaround.  However, I really want to know why FCPX is reading from the backup drive, is there anyway to just tell it to ignore the drive without mounting it?  I could just remount the drive before i leave for the day but thats something that i could forget to do. as in yesterday when i got 20 minutes into my drive home and realized i forgot to reconnect. 
I know this seems like a "laziness" question but it really does worry me that final cut gets confused as to what projects are on what drives when both are connected.  It wouldn't worry me as much if both drives showed an identical projects list, that would make sense and i would have ignored it from the start.  But the fact that every time i restart final cut the projects are randomly visible or not visible on either drive really makes me worrisome.

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