Before upgrading a ZD you should read the release notes and check the version compatibility.
For 10.1.0 GA https://support.ruckuswireless.com/documents/2149-zonedirector-10-1-0-ga-release-notes
9.12 was not a supported upgrade path to 10.1. This means the configuration of 9.12 cannot be converted directly to 10.1 so an intermediate version must first be used. This was why your ZD factory defaulted when upgrading.
The backup restoration is under the same limitation due to data base migration. You can only install a previous version of configuration backup that falls in the upgrade path.
The only way to restore your backup is to downgrade to 9.12, 9.13, 10.0 (which is in the upgrade path), restore the backup taken in 9.12 and then you can follow the upgrade path to the version of code you wish to run. You only need to choose the oldest version of minimum code level for the new code as intermediate version to upgrade from the unsupported version. Always choose the version of code with the highest third digit as these indicate Maintenance Releases and will have the most code fixes. 9.13.3 is the third Maintenance Release and is better to use the 9.13.0 (GA), 9.13.1 (MR1) or 9.13.2 (MR2). Check all the previous version release notes to find the least number of intermediate upgrades.
I hope this information clears up your issue.