When Highlight is used for delta analysis such as in the context of agile methodology, the folder structure should remain the same across versions/sprints/iterations/scans, since it is used to cipher scanned files.
For each file Highlight scan, a unique signature (a CRC – Cyclic Redundancy Check ) is calculated. When a new scan occurs for the same file (same name and path), Highlight calculates a new signature. If both signatures are identical, it means that the file hasn’t changed between the first and the second scans. If the signatures are different, it means that the file has been modified between the scans. If a file wasn’t there in the first scan, it obviously means it has been added between the two scans.
So when scanning the code with the Local Agent or CLI ensure that the folder structure remains the same across versions, as it is used to cipher scanned files. For eg C:\src\version1.0\myfile.java will be considered as different from D:\src\version1.5\myfile.java, and myfile.java will be considered as a new file in the second scan.
More details can be found at How to estimate size and health of high frequency code iterations using the delta analysis feature