*** SOLVED FOR ME ***
Rig is Mac Mini 2011 / Thunderbolt Display / Westen Digital Thunderbolt Duo (daisy-chained to Display's additional TB port). Constantly ejecting Western Digital 8Tb Thunderbolt Duo also causing display instability after 10.10.5 update. I'd been documenting my pain over at Mac Mini Thunderbolt Display Instability 10.10.5 before discovering this discussion.
My steps to resolution have been as follows:
1. Perform SMC reset specific to your Mac.
2. Shutdown and disconnect Mac / Display from wall power.
3. Disconnect all peripheral connections except TB video cable (if Mac Mini).
4. Connect wall power. Boot Mac. Wait 10+ seconds before logging in.
*** Your system should now be free of display flicker issues caused by external HD instability ***
5. Shutdown cleanly and disconnect Mac / Display from wall power.
6. Disconnect video cable (if Mac Mini).
7. Connect TB drive cable to TB Display & Storage Unit. Attach Storage Unit power.
8. Connect wall power. Boot Mac. After chime, connect video cable (if Mac Mini).
9. Wait 10 seconds before logging in.
*** Your should now be able to see external HD attached (in my case) via Thunderbolt cable ***
10. Access System Preferences -> Energy Saver. Set both slider controls to ‘Never’.
11. Access System Preferences -> Spotlight -> Privacy. Deny access between Spotlight and External Storage.
12. Rescue External Storage content (if applicable).
13. Remove Western Digital Drive Management Software from Applications.
14. Format External Drive / create new RAID set using OSX Disk Utility.
15. Shutdown cleanly. Boot Mac.
16. Access System Preferences -> Energy Saver. Reset defaults.
17. Access System Preferences -> Spotlight -> Privacy. Deny access between Spotlight and new external HD Label created in Step 14.
*** Stability returned to rig ***
Thank you to all for support and encouragement. I hope these steps help someone out there with a similar setup.