Hello fellow school master of tech... I got nothing. IMO, SCCM has gotten to the point that it's easier to just backup and rebuild than it is to worry about some "P2V" converter screwing something up, at least for smaller setups like the one I maintain. But then again, if you have the capability of converting to a test machine, checking with the SCCM Toolkit to verify everything was transferred correctly, it's worth a shot. Please note, what follows is what worked for me, not necessarily best practice or recommended, but this worked for the most part so I'm sticking with it. If you do decide to do the backup and nuke, what I did recently was go through the Assets & Compliance and Software Library workspaces and exported anything that I valued (collections, Compliance Settings, Applications, Packages, Driver Packages, Task Sequences). SCCM will export anything it needs for them to the location you specified, you can skip exporting the content assuming you will rebuild the server with the same shares. Once everything is exported, build the new SCCM server w/ any required fixings. Once the new SCCM server is up and running, migrate the files from the old server to the new and setup the necessary shares. Go through the workspaces and import the exported items. When it comes to the Collections, SCCM tends to derp and has no error checking on if it is using a user collection in a device collection and will cause a bad day, if you run into this, check what I did to fix it https://www.windows-noob.com/forums/topic/14002-imported-device-collection-using-user-collection-as-limit/#entry53677.
This is in no way a bullet proof method, there are some things that I am still cleaning up like some imported packages are not being distributed correctly, but re-making the packages manually fixes that.
Hope this helps, if you need more help, let me know, us school admins need to stick together!