It is safe to install this version of the Proxomitron over-top of a previous version. However, BE SURE TO MAKE COPIES OF ANY PREVIOUS CONFIG FILES YOU WANT TO KEEP FIRST! Especially if you've made modifications of your own.
You can also rename them to something other than their original names (as in default.cfg to MyDefault.cfg) or place them in a subdirectory of their own. Otherwise any changes you made to these config files will be lost!
Only the config files included as part of the original distribution are replaced, any files you named yourself will be safe.