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Boot Issue With Secondary Hard Drive

Pippy Longsocks
I'm trying to add an SSD with Windows 10 as a secondary drive. Currently I am running Windows 7 on an HDD. I'd like to keep my original drive intact and simply boot to the SSD to get to Windows 10. I have my rig set up that way now, but when I boot to the HDD to get back to Windows 7 it wants to run CHKDSK on startup. I'm hesitant to allow it to run because it's only trying to scan the SSD and it really has no business messing around with those files. When I boot from the SSD to Windows 10 there is no issue. Is there any harm in allowing Windows 7 to run CHKDSK on the new drive?
 
This is essentially my question. The novel that follows is just more detail that may or may not be relevant but this is how things went down. 
 
My reason for being hesitant to run CHKDSK is because during my first attempt at setting this up I installed Windows 10 on the new drive with the old drive still installed and it didn't put any boot files on the new drive because they were already there on the original. So my system was set to boot from my original HDD first and then gave the option to launch either operating system from there. This isn't how I wanted it set up. It was difficult to tell which operating system was which because they both were listed as "Windows 7" even though one of them was Windows 10 (I suspect this is because I installed Windows 7 on the SSD first to get online and download the Windows 10 installer). Also, my preference was to be able to boot directly to the drive I want to use without any detours. My original HDD is old and having the boot files for both hard drives stored there doesn't seem smart.  
 
So in the process of trying to sort this out I tried to boot to Windows 7 out of a restart from Windows 10 and the computer crashed. I think this is because I didn't turn the computer completely off first. Lesson learned. In any case, after this happened the computer prompted on boot to run CHKDSK when I booted from the HDD and it did the same when I booted from the SDD. I allowed both scans to run. I later noticed that I had I lost the ability to boot to Windows 7 from the HDD. Booting from the HDD brought up the menu to choose the OS, but both choices loaded only Windows 10.
 
Now I have both operating systems installed completely separate from each other. Each drive has its own reserved boot files. The boot to Windows 10 from the SSD is good. The boot to Windows 7 from the HDD prompts for a CHKDSK scan and it only wants to scan the new SSD. I'm not sure if it's doing this just because it was recently plugged in or there is something more worrisome going on. I can skip it and everything seems fine. I'm using the OS on that drive now.
 
I've read that you can edit the registry to stop Windows from automatically running CHKDSK, but I'm trying to avoid taking such an extreme measure. So this is my predicament. I'm nervous to allow CHKDSK to run and I instead skip it when I try to boot to the old drive, but ideally I'd like to stop being bugged by the prompt. I'm also nervous that maybe there's a good reason its trying to run CHKDSK and letting it just finish would resolve the issue. There was actually a third installation attempt where I had everything set up after allowing CHKDSK to finish on both drives and it worked. But my computer wasn't recognizing the SSD as an independent boot device so I had to start over and now I'm in a similar position with everything working but getting nagged by this CHKDSK prompt again. 
 
The end
 
Any help is appreciated!
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