Reconstruct keeps track of different versions of BIM models that were uploaded to the system. Reconstruct uses the filename to identify different versions of the same model. If you change the name of your BIM model file before uploading, it will not be marked as a version of an old model. For this versioning system to work, you should upload files with the same name. For example, if you upload the first version of your mechanical model named "Mech_Model_Proj.rvt", then the second version should have the exact same name to be marked as version 2.
In Reconstruct Data Manager, you can group BIM models by name, which will show you the latest version of each file.