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Each time AboveSoft Adaptive Estimator loads, a unique CRC-32 number is calculated for each branch of nodes of the loaded template, so each time you save a Project this unique number is saved along with the Project for each of these nodes. If -for example- someone modifies the number of minutes assigned to a True or False question by changing the template, this unique number will change for that branch, and the next time you open that Project those nodes will appear as "Unclassified nodes" (except if node validation is disabled). The next figure clearly shows which nodes represent a branch:

From the "Options" menu you can disable CRC-32 validation. This may become your previous estimation inconsistent since some changes on the template might have changed a node meaning or the way a value is measured. Use it at your own risk if you are sure that the file will still be consistent. Some nodes will still end up as unclassified nodes if their definition is no longer available in the newest version of the template.