Why might the Compare function in EPMA produce thousands of deletions and re-additions when expected

A metadata change was attempted recently for an application in HFM 11.1.2.3 by importing a new metadata file to EPMA, using the same file and procedure as always and this file only contained a very small number of changes.  It imported successfully in the Development environment and when compared to the deployed application, only the few changes appeared as expected.  However, when the same file was successfully imported into EPMA for the Production environment, the Compare to Deployed Application function produced thousands of differences - basically deleting all entities, scenarios, years, etc and re-adding them again.  Any subsequent import of