We seem to find the easiest way to update slic3r in repetier is to backup and then replace the slic3r directory inside the repetier-host program folder. This keeps everything where it expects it to be, including your config files!
e.g.
(1) Rename "C:\program files\repetier host\slic3r" to "C:\program files\repetier host\slic3r.OLD"
(2) Unzip the downloaded version of slic3r to "C:\program files\repetier host\slic3r"
(3) Run repetier host and check that everything works
If you have any trouble, you can always go back to the previous version by undoing the steps above.
SD3. Mk2b + glass, heated enclosure, GT2 belts, direct drive y shaft, linear bearings, bowden-feed E3D v5 w/ 0.9° stepper
Smoothieboard via Octoprint on RPi