ESFRAME:
To prevent issues it's adviced to install a second version of Windows with only the blank HDD/SSD in the computer (First OS drive removed or disconnected). Later when you add the previous HDD/SSD to the computer, boot the OS you want to have as default, using the BIOS boot drive selection and install EasyBCD on it, to create the Windows dual boot.
BadAsAl:
When Windows is installed on GPT partition table, the installation can take several partitions (Boot, OS, Recovery, System Reserved) that can be set on a second HDD... this seems like what can cause updating one OS can affect the other's boot process. To avoid this type of issue, it's best to install when a single OS drive is in the computer. What you can do now is find out which partitions belong to Windows 10 and which one to Windows 7, and move them to the right SSD. I don't exactly know how to move them but I'll look for the information and post it here*.
You can use EasyBCD to edit the bootloader and create the Windows dual boot selection screen, and you can stop using the BIOS boot drive selection screen.
EasyBCD Community Edition
http://www.softpedia.com/get/System/OS-Enhancements/EasyBCD.shtml
*This should help "relocate" (at least) the Boot partition or the Boot files contained in it.
(System Reserve is another name for the Boot partition)
Windows 7: System Reserved partition on wrong drive - how do I move it?
http://www.sevenforums.com/installation-setup/189387-system-reserved-partition-wrong-drive-how-do-i-move.html
And apply these suggestions to relocate the System Reserved partition.
How do I move System Reserve partition?
http://www.tomshardware.com/answers/id-2339773/move-system-reserve-partition.html