Hello photoscan_user,
Rehostable license activation assumes creation of the additional directory:
for Windows: C:/ProgramData/Reprise/agisoft/photoscan-pro/
for Linux and Mac OS X: /var/tmp/agisoft/photoscan-pro/
(default paths can be altered by setting AGISOFT_REHOST_PATH environment variable prior to activation).
This directory cannot be removed or modified, as such actions would affect the license validation (lic file without this directory wouldn't work).
The steps that you mention: start server - activate PhotoScan - deactivate PhotoScan - shutdown server - looks safe.
Some configuring of the cloud-based server may be necessary, if you want to use GPU acceleration, or enable GUI mode (requires OpenGL configuring).