Well, I did find part of the solution myself... The Source representative seems to generate a list of files on the source every 40 minutes. This XML file is stored in C:\ProgramData\vulscan and is named something like sourcePath.manifest.xml.
Deleting this file forces the source representative to re-list every files on the source. May come handy when running tests...
Still, I did not find how we can change those 40 minutes. Does anyone have a clue on this?
In a discussion with our developer, here is what he had to say regarding this matter:
"The source representative creates and caches a manifest of the source’s file list, storing that information in the representative’s programdata\vulscan directory. It only regenerates that cache when asked for the same information later AND it’s been 30 minutes since the last request for the information. If you put “/force=true” in the registry version of the commandline, then I believe the manifest would be created on every request. The delay of 30 minutes cannot otherwise be configured."