Server is meant to print over usb only. Only that way you can benefit from all the cool features. Of course you can store with host to sd card and start sd print but then all you can do is watch temperatures.
Printing from server is normally very stable and only real problem with W10 is that you can not prevent windows from updating and rebooting.
So first you should find what the problem is and then hopefully fix the source of it. In server in web frontend you have a printer menu with log entry. There you can enable logging and later download the log file and check it for errors. There is also a general server log under c:/ProgramData/Repetier-Server/logs whcih also show special things happening. Both together might give the required hint.
If you have repetier-firmware you can run tests without real filament usage by enabling dry run (in host manual tab or by sending M111 S14) for testing. In some cases this works and real prints not. That would indicate heaters introducing the problem either by induction to usb cable or power (voltage) going up/down from the switching of heaters. If it drops too low it might stop usb communication completely. You see this simply because you can not connect again to printer without unplugging usb and unpowering printer.
