I recently had a spate of disconnects and thought it might be related to my new iMac, but cured them by power-cycling the TB3 dock and disconnecting all Thunderbolt cables and blowing out connectors and sockets with compressed air (at least it appears to be cured).
The Questionable Thunderbolt chain contains a Cable Matters Thunderbolt 3 dock, a OWC Thunderbay 4 with four drives in JBOD mode, a TB3 <-> TB2 Apple adaptor, and a OWC Thunderbolt 2 Drive Dock.
Maybe Catalina is more sensitive to briefly intermittent connections?
The TB3 dock only has two USB 3 connections currently as I’ve recently had a 7 port hub failure on one of the charging ports which has been replaced by a 10 port hub with 5V 2.1A per port. The two connections are a OWC Blu Ray burner (on) and an ASUS Blu Ray burner (powered off).
I’ve had three disconnect events within a week, one causing a kernel panic. After each event, I had to manually check all connected local disks - twice for APFS disks as there seems to be a boot mount and a data mount now. These checks range from practically instantaneous for boot mounts to hours for the local Time Machine disk.
I also purchased a CalDigit Thunderbolt 3 dock to replace the Cable Matters unit in case this disconnection event occurs again - I’ve had issues with Thunderbolt docks overheating in the past cured by replacement of the dock (OWC’s Thunderbolt 2 dock comes to mind which was sorta replaced by a Sonnet Echo 15+ dock). This can be redeployed for my MacBook Pro 16 if the power-cycle of the Cable Matters TB3 dock proves to be efficacious.
I also had a spate of NAS disconnect failures which were eventually cured (I think) by replacing the ribbon ethernet cable (supposedly CAT7 cable from Amazon) with a Cable Matters thicker cable from the iMac to the Orbi RBS850 satellite. This was another problem which took about 60 diagnostic steps to identify changing everything from the mount protocol (SMB or AFP) to reconfigurations of the ethernet adaptor to reinstalling the running system.
The Thunderbay 4 is the result of drive dropouts when my primary was a 2017 iMac 5K from 3 USB 3 external hard drives which became two TB3 OWC Mercury Elite Pro units in JBOD and finally the TB3 Thunderbay 4 unit in JBOD. The enclosure change was made in an attempt to cure the disk dropout problem and simplify power and data cable routing and (possibly) increase speed.
All fingers and toes crossed - the disconnections appear to have stopped.
The long and the short of it is that all my disconnect issues seem to have been cured by replacing marginal cables with known good ones, and disconnecting all cables and blowing out plugs and sockets with compressed air (I use cans of Compu•cessory purchased God knows how long ago.) My problems may be of my own making - I do smoke in my office and smoke particles may infiltrate my low voltage electrical plugs and sockets.
Environment: macOS 10.15.6 Build 19G2021, 2020 iMac 5K, core-i9, AMD Radeon Pro 5700 XT 16 GB, 4 TB SSD, 10 gb ethernet, 128 GB (non-Apple).