I don't know what options you set with Acronis.
You have ended up with two conflicting OSs and probably assigned the 1st HDD disk signature to the 2nd HDD. Windows will reassign one of the disk signatures. Bottom line is you end up with a mess.
To get back to your original state. Mark the active partition on the 2nd drive inactive and either:
1) Run system repair up to 3 times on the 1st HDD (preferably with the 2nd disconnected) or
2) Reimage 1st HDD with the image you have on the 2nd HDD.