It is only possible to upgrade all the site collections that have New Upgrade package (7.1.5.xx+). 

If some site collections do not have the New Upgrade package (you did not proceed with the first upgrade), you will have previously installed ShortPoint version there.

If you want to upgrade some site collections that already have the New Upgrade package (you reinstalled the app there), it won't be possible. You may disable Auto Upgrade and once the new ShortPoint is available, check the changes in the Sandbox Mode.

After you check it, you can upgrade to that version or discard and stay on the current version you have.

Related articles:

Main articles about New Upgrade:

You may check other FAQs about ShortPoint Upgrade in this folder.