No risk as long as one keep separate versions of both libraries and project files in a separate folder trees for ver. 6.01 and 6.99, and use the 6.99 development builds for testing only and not actual work. The 3D models are “read only” so no need to duplicate those, as long as all installs are performed without upgrading libraries.
In this case it was useful to look a little forward: I might consider to eventually do a global search and replace in the 6.01 project files and personal libraries to substitute “KISYS3DMOD” with “KICAD_USER_3DMODEL_DIR” or something equivalent, so that when I finally upgrade to 7.0 perhaps a year from now, I can keep a separate locations for my personal 3D model repository and those in the official library.
Edit: Here is a useful link in this regard: