A log file saved with VemsTune contains the configfile and therefore the VE map is known, so the analysis will suggest alterations to that VE map. The log also contains configuration changes, I'm not sure if/how that is taken into account when the analysis is made. My point being, don't make any changes to your VE or lambda target map while datalogging if you wish to do analysis later. Do it in steps. Datalog, analysis, apply changes, .. etc.
The SD card logs do NOT contain the config, so you need to load a save config of the one used when the SD card log was made if you want to do any analysis and alter your VE map. VemsTune makes a point out of this when you open a SD card log.
As with other things in VemsTune this is a moving target, bear that in mind and suggest stuff and ask away if the function is not clear or needs enhancements.