In the Flash version of VRF, there is a survey feature that allows you to take surveys from static clients that would then assist in providing floor plan attenuation data for location calculation. This feature has not yet made it into HTML5, and is on the list of features still to be ported over.
If you don't want to swap back to Flash, you can make use of the AMC client (check it out on your AMP's Home -> Documentation page). The AMC client runs in the background of Windows laptops and uses the laptop's wifi to collect data and report back to AMP (similar behavior to APs in sensor mode).
The swap between Flash and HTML5 should not affect AP location. That sounds like a defect. Please open a support case to have support take a look.