This fix is going to involve moving the changed data from the SSD to the HDD so you can then do a clean install on the SSD.
- Move data from the SDD to the HDD
- Verify data on HDD
- Swap HDD and SDD (SDD to be internal)
- Wipe SDD and do a clean install of OS
- Migrate data from SSD to HDD
- Set up CCC to clone SSD to HDD as backup.
You should have the following:
- USB Installer of macOS Sierra or OS X El Capitan
- Preferably a different HDD (you only need a 250 to 300GB drive to backup the SSD)
- A backup of your Keychain
- A backup of your Application Settings where applicable
1. Move data from the SDD to the HDD
In your comments you said that the data on the SSD changed. You need to copy over the user data from from the SSD to the HDD.
Preferably, you should have another HDD to do a quick clone of your SSD as an extra layer of insurance. However, it's not absolutely necessary.
To move your data from the SSD to the HDD you need to create a directory on your HDD somewhere and call it SSD Data Backup or something that identifies it as where it came from. You can do it in your home directory, it really doesn't matter, just so long you know where it is. Then go into the SSD
/Users/ directory and copy over your entire directory to the SSD Data Backup you created earlier.
2. Verify data on HDD
Make sure that everything you copied over from the SSD is on the HDD. I can't stress this step too lightly. Once you proceed there's no going back.
3. Swap HDD and SDD (SDD to be internal).
Now that you have a backup of your SSD data on your HDD, it's time to swap out the drives. You should now have the SSD internally and the HDD externally. Don't connect the HDD until you have finished step 4.
4. Wipe SDD and do a clean install of the OS.
Delete the partitions, everything. You need to have a single partition so that when the OS is installed, it will create all the necessary partitions for you like the boot partition, and the recovery partition. Set it up like you just got it from the factory.
5. Migrate data from SSD to HDD.
Once you have your new OS installed on your new SSD, it's time to move the data back. Attach the HDD (now external) and you can copy things back. You can use:
(I personally go for the third option because it allows me to do a genuinely clean install)
6. Set up CCC to clone SSD to HDD as backup.
Once you have everything setup to your satisfaction, you can now use CCC to clone your SSD to your HDD. Keep in mind the way CCC works is that you clone your drive to an external for backup purposes. If/When things go sideways, you get a new drive and clone FROM the external to the new, not swap.