There are a couple of different things at play here which can confuse things!
To start out we have the upgrading of the APFS file system that took place with High Sierra. So ALL SSD systems where forced to it and you where not given an option not to during the OS install or upgrade! There is a patch you can apply to the installer to prevent this though. This can play havoc if you have older OS’s that you boot the system up with. As an example all of my tools thumb drives are based on older OS’s and can’t access the new file system to clean it or fix things. If I upgrade them to High Sierra then I can’t access them with my older systems! What a mess! Now for a lot of people this won’t in its self be a problem unless they encounter a problem with their system.
So here’s the rub! Your logic board dies and you replace it and now you can’t access the drive! The reason is the systems firmware was also updated with the original logic board and this replacement still has the older firmware which won’t allow it to boot up under APFS! I’ve seen two cases of this here alone Hard Drive Not Recognized After Replacing Logic Board & Why won't my MBP boot from the ext SSD.
OK moving on… The next one is High Sierra by default sets up your Desktop & Documents folders as an iCloud shared space (syncing the files). So when online your system can act wacky as it’s so busy trying to copy up altered files it stalls out! This is more of an issue with SATA based drives as the number of queued actions is more limited than PCIe/AHCI and PCIe/NVMe based drives (SSD’s). This appears to be hitting SSHD drives hard! (Seagate) I did some network tracing at it became clear the drive was not able to handle the delayed queue’s.
So you need to undo the setting in Preferences > iCloud - Uncheck iCloud Drive or open it and uncheck Desktop & Document folders (which is what I do)
The real issue here is Apple is not testing or thinking of older systems in the base configurations. These issues are also seen in the mSATA based systems (Mid 2012) Gen. 2A per The Ultimate Guide to Apple’s Proprietary SSDs.
I do think this is one of the reasons APFS was delayed! As Apple feared the ramifications of so many systems still out there that would have problems. And again its only those who had upgraded their drives from HDD’s to SSD or SSHD’s! Is this recoverable YES! It’s only you need to turn off iCloud document sync.
I’ve searched high and low looking for something in Apples TN’s and developer sites and so far nothing has been written explaining this issue! So I do fault Apple for lack of follow through explaining things. But thats a typical Apple move not telling anyone anything that might bite you.
While I think this is nasty, I don’t see this as a way to undermine independent repair. As this issue is also a factor with a still supported system with its original drive! I would fault the failure to Apple’s Quality Control Dept. Haven’t we seen as of late quite a lot of QC issues! The iMac Pro VESA mount with crappy screws! The failure with the newer MacBook & MacBook Pro keyboards! The failure to catch a driver signing issue with the newer i9 based system, and let alone it shouldn’t have been sold in the newest MacBook Pro ultra thin frame as it’s thermally throttled! What a waste! Then the Display ribbon cable failures on the new TB & Fn models Black shadows from the bottom of the screen & Stage Light Effect on Display Screen and now the defuser sheets are peeling off the back of the display black bar at the bottom screen. Thats just the hardware issues from QC. Now think of the added costs lack of repairability will have to Apples bottomline once the numbers of all of the uppercase swap outs & displays is released. Oh, the 2018 models still are having keyboard issues! So they will be a QC problem that will continue.
Yes, I’m not happy with the QC failures are they are all very obvious failures from the get go! And yes the lack of serviceability of these systems will shock Apples customers in the next few years. I’ve already had to post answers which I shouldn’t have had to! Sorry you need a new $800 display because a cable failed or your logic board has failed and you need to go to Apple to have them recover your files from the soldered down SSD or there is no way to gain access to your files at all after your system got wet. So going forward with a newer TB or Fn system is a pointless exercise if you don’t want a throwaway system.
Apple has truly lost its way! I see it going the same way Iomega went! Early Iomega Corporation History And where they ended up LenovoEMC They fell victim of their own success as well! Had a great product then the $hit hit the fan with failure after failure. So sad… Couldn’t fix their failures when they tried to go in to new markets as the product was not durable like what they had in the past.