Issue will be fixed in software 5.12.3 which is forecasted to be released in the first half of April 2019. Please note that release date is tentative and may change.
Actions to alleviate impact:
Disable auto save. By disabling auto save when unit 2 becomes temp base the system will not automatically save the stack's configuration with ISIS disabled. If the configuration is not automatically saved the user can recover ISIS by rebooting the entire stack rather than having to console into the stack to re-enable ISIS.