We need to know what you have checked before we can suggest places to go next.
We also need to know exactly how you have the smb scan setup.
I use SMB scanning using a Konica/Minolta b458 using a service account that has limited rights to a scans folder in each user's home drive.
I've never seen this for home drives.
I CAN see this happening for some of the scans that go to a group folder where multiple users have access to the scan folder and accidentally delete or move the scanned document elsewhere.
I can also see this happening if you have document control / security tool / backup that is getting triggered.
and last I can see some weird issue with file access rights so you can create a file using the copier but can't open it from your own machine.
I don't remember all the details but years ago someone ran into a weird issues with scan to smb where no one could open files scanned from a particular copier.
Turned out it was setup with an account that could create files but no one could access and the created files were hidden. The administrator could see the files but no one else could.
The admin thought everything was fine, while his users thought it is was broken.
Main machine: Core I7 -2600K @ 4.0Ghz / 16 gig ram / Radeon RX 580 8gb / 500gb toshiba ssd / 5tb hd
Old machine: Core 2 quad Q6600 @ 3ghz / 8 gig ram / Radeon 7870 / 240 gb PNY ssd / 1tb HD