nope, no system restore or anything like that, the pbx is installed on a 'headless' PC (no keyboard/mouse/monitor) in remote location (I live in Canada and the PC is in EU at my parent's place) and I use it primarily to run security cameras (those run on special hardware PCI card) but l didn't even have that running when I installed Axon and started setting it up with SPA (also in that remote location), it runs very few programs otherwise, I just figured that if I have such PC running around the clock there, I might as well put the pbx on it too to give it something to do
PC is last year's build, Asus mobo N4L-VM DH for the new CoreDuo mobile processor - I got lower end T2400 just as they started shipping last year (the idea is to have low power PC since it is supposed to run 24/7/365). I have WinXP Pro lightened version running on it but it is fully functional even for your everyday personal PC, it is not some customized barest bones system and so far its been behaving nicely the whole winter...
I have 3CX pbx installed on the PC, that was the win pbx that I started my experimenting with at first some weeks ago but I had poor quality initial calls (jitter/echo, even flaky connections... it had problems with my NAT apparently -> I run remote (WAN) extensions that are behind their own NAT) and so I tried Axon, I didn't uninstall 3CX but just disabled its services and put it out of the way before I installed Axon just to be sure there wouldn't be some interference (like ports use etc), don't see how that could have anything to do with this loss of configuration, Axon seems to be more agressive on NAT traversal and I like that and it seems to work for me - I tested Axon so far just making calls to myself (via remote access to that PC which gives me full control of it) and recording my calls there and downloading them to listen to how they sound here in Canada, today I am still to test the phone connected to SPA3102 there
Axon logs don't show much any cause at all, like what might have happened, after all such funky event is not part of telephony messages that it logs, logs just started coming up at a given time with those messages about extensions trying to register and that you should make extensions in Axon for them to be able to get registered... that was my SPA trying to register its FXO/FXS lines with Axon but there were all of a sudden no extensions for it anymore
as I said, after figuring that I am somehow back to User: Admin and no pass login I managed to log into its web configuration (I do that locally only, as if I was sitting at that PC out there, ie., I never enabled remote web access for Axon since I don't need that given I can directly and fully control the whole PC it is installed on using 'RemotelyAnywhere' secure remote access) and I found no extensions whatsoever, no external lines, even those post install lines that get premade for skype uplink and Carousel... simply cleaned out Axon with only logs left in it, if it wasn't for them, I would have thought I dreamed it all 
I exported and marked up relevant Axon logs and I think now perhaps it has some clue as to what might have happened, just before the loss of settings, the SPA is logged as "SIP Trace", I am not sure where that (separate) log came from, if it was requested by Axon from SPA or if SPA sent it to Axon on its own or if I played with the setting in the Axon on Logs tab where you have that link "Advanced SIP Tracing", maybe I checkmarked 'Log all SIP messages' but I am not sure if I did that, anyway just after the SIP Trace was done, the Axon seems to have restarted and when it came back it was more than pristine, it was cleaner than just post installation state, I did make couple extensions then to get the SPA registered and it did but then I thought more about it and decided to deinstall and install again and it brought all those COnference, On hold server etc premade extensions back along with regular ones
you can download the formated log here: [Anomalous_Loss_of_Settings_in_Axon Log.rtf](ftp://mir2.pointclark.net/Anomalous_Loss_of_Settings_in_Axon%20Log.rtf)
vanDivX