I think I know why my desktop isn't working properly. Because someone stole my 1TB Windows HDD and copied it onto my 2TB Linux HDD. I don't know who, how or when they managed to do this but its gone.
Wow, that took quite a bit of effort & enormous risk to accomplish, you obviously have a certain timeframe of being away & someone took that opportunity to do this.
99.9% of thieves would had outright stolen the drive (or the whole computer) & ran with it, not taken the risk of being caught in the midst of a break-in, which can have very bad consequences. Let me come home & catch a thief here in the act, there'll be no need for an ambulance, call for a body bag, because when I go somewhere, even if I can't carry in a weapon in an establishment, will leave it in the car & put back a coat of some type that I always wear outdoors upon getting back in.
I've been broken into once & learned a lesson. There are several of us neighbors who watches one another, from the front, side & rear, all we have to do is pick up the phone call any of the others when leaving for awhile & will get a call if something's funky going on, as well as 911 if a crime is taking place. I promise that #1, should I arrive before the cops, no one will be shot in the back fleeing to make me the criminal, one way in & too many obstacles (very hidden window & patio door locks other than the latch) not to meet face to face trying to flee & #2, will wait until the suspect is under full control before calling 911, if not on the way. A break-in is just that & we have a lawful right, approved by our own Sheriff to stand our ground.
Plus being disabled, no jury would find me guilty upon sight of my physical condition, as long as it's a face to face confrontation, plus have webcams installed & am adding a couple more.
In your case, I suggest to #1, find a safer area to live & #2, establish contacts with trustworthy neighbors, preferably homeowners who are long established residents to watch when you're away.
As far as the crime goes, no doubt the criminal either is someone you know & may trust, or another you don't know that monitors when you come & go, still a very odd & high risk crime. Breaking & Entering into a home is a felony in progress, often termed 'midnight burglary' if anyone's at home, a more serious offence, the one doing so carries a huge risk in spending that much time in your residence.
So I suggest to reevaluate who your friends/contacts are & if you can't move, secure your living area better. There's ways to fully secure your place for under $100 in parts, to include deadbolts on the doors with the plate on the other side having two very long screws drilled deep into the studs (after a few inches, pull the bit out & squirt plenty of Locktite in & finish), add hidden locks in windows, a couple of secret, yet well concealed & strong pins per window. And don't show anyone where these are. Friends, family, neighbors and/or the accomplices of any are often the ones that took the chance described here. Not a typical criminal where the goal is a 'quick & dirty' execution of a crime & get out of the area as quick as possible to avoid capture.
To answer the above, I also don't believe that the police would go through that much trouble to seize your HDD over an alleged crime (hearsay). You would have had been served with a search warrant & any computers, external drives to include USB sticks, as well as optical media, would had been seized in your presence, provided that had you been there, no violence would had been predicted. At any rate, you (or a known family member, if none known, then your landlord, on your behalf) would had been notified in some way that your HDD was seized as evidence to investigate for possible crime(s). A suspect of a crime has full rights until conviction, to include being present with attorney during search & seizure of property. If you believe this to be the case, you need to contact your local law enforcement agency & ask if you're under any investigation. If so, most any attorney worth retaining would agree that your rights as a citizen has been violated by this type of search & seizure of property.
Only in the case of (suspected) high crimes committed against the nation, would law enforcement seize your computer equipment & most likely, you as well.
Sounds like someone you trust has pulled a dirty prank, although note that this is only my opinion, and yes, whoever done it needs a good 'wake-up' call in the form of a butt kicking. It's been close to three years back, that's exactly what happened when a relative stole a USB stick from me that had been used as a portable Malware scanner. There were a lot of infected files quarantined, he stole & traded it to a local store owner for a pack of cigarettes. Not only did he receive a severe butt kicking from that man for his PC being infected, when my other relative (his mother) demanded who done it, he told her, she went to the store & demanded to know why, he told her straight up what happened & showed the USB stick. At that moment, she knew it was mine (made of metal with a streak of red nail polish he didn't remove first), as I had just cleaned up her computer days earlier. When she returned home, he got at least two more whacks across the head with a broom handle for being a thief & called me to pick up my USB stick. She knew I was looking for it because I called & asked if I had left it laying on her desk, a couple of others also knew it was missing.
So I suspect something of that nature, someone you may know & trust, did this to you, not the local authorities.