If you get a Bootmgr is missing message, the boot is not being directed toward the proper boot device. Is the SSD always recognized in the Bios or could it be dropping out of the available boot options list?
Are both drives SATA?
Do you have the Install Media you could boot to? If not, you might try downloading a Windows 7 DVD with SP1 included. Then boot to it and run the Startup Repair from the options. And it may take several tries. But if the indication continues to happen, possibly your boot device is not stable or being corrupted.
I will assume you are using a MBR configured system and not related to UEFI?
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