TC hard disk has always had 3 partitions.. It is very typical of disks in every device now.. same in your Mac the drive has recovery boot partition which is hidden. They are minimal size..in 2TB drive the min size partition is 1.07GB so you lose 2GB out of 2000GB.. And when the disk is not present the same thing is created in memory to hold files that are required in operation. much smaller of course because the memory size is so much smaller. APswap and APconfig.
See Upgrade & Partition TC internal hard disk - info howto
And then... the "may be overheating" warning came up again in Airport Utility on the TC withing minutes of turning it on
The overheat stops the TC internal disk working.. not the other way around.
I don't blame the genius.. Apple tell everybody the min they require to do their jobs. It is just that I have played extensively with the insides of TC.
Repair AC version Time Capsule or Extreme - LaPastenague
I am also pretty sure you have a dead sensor.. or faulty power supply..
Anyway .. it should continue to work as a router even in overheat condition. Apple turned off the hard disk during overheat as that would greatly contribute to heat load.. I have managed lately to get around it.. since the actual overheat warning is faulty sensor.
So buying a fresh drive to put into the TC would likely be a waste of time (sigh)
Yes.. it would be a waste.
And I would not recommend extensive repairs of the Gen5 TC. It is very delicate. And the plugs and sockets not really designed for robust usage.
(I have a second backup done by a still working 3rd gen TC).
Gen3 is perhaps the best TC they made. Except it used a samsung pinpoint 1TB drive.
It has occasional strange faults.. but they are rare.. the Gen4 has a much more common soldering fault. But if you want a TC for backup in your basement.. let me recommend you up size the drive in the Gen3. They are much easier units to work on.. a 2 or 3TB green drive will do wonders to it. Turn off the wireless.. and just use it on the network for storage. I bought a couple of cheap second hand Gen4 to do exactly that. One I have fitted with alternative power supply and 5TB drive. All there on my website if you like to take a look. Mind you I needed to bake one of the boards.. but that is so successful I have no problems still recommending it.
Apple should write up some recommendations as they are leaving us in the lurch by discontinuing the whole product line. Sorry, but "backup in the cloud" isn't an answer for me.
I agree about the cloud. It is not a great solution for a disk failure in the Mac.
Let me suggest a few things.. long experience on these threads about the airports.
1. A number of us here have moved to Synology NAS.
Synology support for Time Machine is excellent. The reliability is as good as the TC.
The cost is a factor. It is certainly a major outlay and IMHO you do need some justification other than backup.. ie using it for file server, iTunes server etc.
Big advantage over TC is speed. Even low end Synology is going to basically saturate gigabit now.
Cheap end NAS do not offer the reliability. Others like QNAP might be equally good.. I just prefer the Synology interface.
You need a router (non-Apple into the future) to go with the NAS of course but that is now a given.
2. USB drive on a router.
While USB 3 is now available on most high end routers and speeds have improved a lot.. most are designed for PC work and use NTFS disks. Only a handful will support HFS+ and Time Machine.
I have Asus router which I have now tested extensively.
It works pretty well. As long as you are prepared to wipe out the backup and start over a few times a year. It fails long term. It can also be very finicky. If Time Machine backup is really just for immediate recovery it could well be good enough. Long term backup that some people are after then no..
Also strange things happen.. latest firmware update of the Asus has caused a strange new twist in the story.
See Re: Time Capsule Replacement
People have suggested the Synology router.. I guess on the basis of similar firmware to the Synology NAS. My reading of it is very little long term testing has been undertaken. What I do see is very slow speeds. Synology are not a router manufacturer in the main.. they might do better to stick to NASes.
3. For the DIYer. A gen3 or gen4 TC setup purely for backup is no bad idea.
They are well built but even the newest gen4 is now 5 years old so lifespan is pushing it. However the DIYer by replacing hard disk when necessary, power supply and capacitors and oven baking can probably keep them going for another few years. Cost is now very reasonable.. $50 or so.. and I would not pay more. The problem is Gen5 TC are not very repair friendly. Actual hard disk speed btw in Gen 5 is not much different to Gen4. The speed tests by Tesserax hold pretty much for either model.
AirPort Disk - Throughput Testing
4. Apple have moved in High Sierra to bring network TM backup in Server extensions into all versions. You can setup a cheap end mini say (2012 version for USB3) with plenty of disk space and should be well supported. In the end I would say this is not a lot cheaper than the Synology. And is basically the same thing.
5. Use multiple USB drives plugged directly into your computer and rotate them.. keep one off site. This is really the best way now with TM unreliability to network drives. But it does mean end user constant involvement in swapping the drives over. USB is fastest cheapest and most reliable with TM now.
6. Get away from Time Machine.
The alternative a lot of us here use is Carbon Copy Cloner.
A small company that does specialise has a lot more clues about what is going on.
See for example their testing of APFS.
macOS may lose data on APFS-formatted disk images | Carbon Copy Cloner | Bombich Software
I get the distinct impression Apple is not testing TM extensively and even the major Mac journals are noticing.
https://www.macworld.com/article/3170844/
Let me add.. I am extremely disappointed in the Linksys.
I might try flashing it with a third party.. but more likely will get rid of it.
I tried to put as much accumulated background and knowledge into this as possible.. so it is fairly long.
And represents my views.. today.