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I've had issues with my Surface losing the mouse, too. Bluetooth mouse. Same with a Lenovo Yoga before the Surface. Bought a cheap HP Bluetooth mouse (HP # H3T51AA) about a year ago & haven't had a single drop since.
It's more my work laptop that I am questioning; and it arises when I intend to actually work from home and VPN back into work. Sometimes the Cisco client just doesn't want to "let go" if I don't power down before re-connecting in the office.
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I'd be blaming the disk controller doing a bad job of power management rather than the OS. And frankly, based on my own experience, I've had much worse luck recovering from sleep sessions than hibernating.
My desktop systems run 24/7 (and have for years), but I always let my laptops hibernate - especially the older ones that otherwise take a long time to do a full reboot. Maybe I'm just lucky, but I've never encountered the sort of situation you're describing.
And I'll bring this up just because I hate them with a passion: Are your drives by any chance misfortune Seagate?
If Windows 10 then I don't believe shutdown or restart really do either of those things. Internally I reckon they sleep and come back as so many times you get your applications back in the same state they were in when you started
That is even after turning off windows fast start in the power options
for ages I think the only real restart is one where updates are installed
For me, depends what my mood is - often I just leave them, so they auto-sleep (like the monitors do). Or I might shut them down - these days, my machines take such a short time to boot (my Lenovo P1 boots in about 10 seconds), it's no hardship to wait through a boot sequence (of course, there's getting your environment back again - Windows could do with a feature like macOS where it'll reopen all the documents/applications you had open when you shut it down).
And most of my machines are on the Windows Insider Fast ring, so get a new Windows version roughly each week, so there's at least one restart a week...
As for docks - I use a couple of Dell Thunderbolt docks regularly and I never power cycle those.
Java, Basic, who cares - it's all a bunch of tree-hugging hippy cr*p
I believe that a computer that is turned off is less likely to have data corruption/loss during mid-night thunderstorm -- mine are always powered off when work is done. The USA Midwest can have impressive night time thunderstorms.
Though I hear before breakfast that squirrels' nuts are a fancied entree.
after many otherwise intelligent sounding suggestions that achieved nothing the nice folks at Technet said the only solution was to low level format my hard disk then reinstall my signature. Sadly, this still didn't fix the issue!