I am having this issue on Thunderbolt external hard drives that are not my external Time Machine. I have a WD MyBook 4TB Raid 1 Thunderbolt external hard drive configured for Time Machine and OS X Yosemite never "puts it to sleep" or "ejects it". But my Buffalo Technologies 1TB Thunderbolt Ministation, randomly (or what appears to be randomly) will put the drive asleep, or randomly eject it and I get that annoying ejection message (why don't we have an option to "kill" seeing those messages...anyways). I can be actively working or the computer can go to sleep, there doesn't seem to be rhyme or reason. The drive will come back once I unplug it and replug it back in. Architecturally, the Ministration is connected to the WB MyBook 4TB Thunderbolt, so it's the last in chain normally. But when I travel, I have I plugged the Ministation directly into the Thunderbolt port and still see the issue. Ruling out issues with the drive a part of a Thunderbolt chain.
I have a call into Buffalo Technologies (WORST TECH & CUSTOMER SUPPORT - I WILL NEVER BUY THEIR PRODUCTS AGAIN) but they are confused on the issue.
I have everything on the Ministation, documents, music, videos, many (but not all) applications. So the Spotlight workaround, though not ideal by a long shot - as I want the Ministation searchable, for now I will put it in the privacy tab to see if the issue goes away. If it does, then WE (like more than just myself) need to call this bug into Apple OS X Yosemite support so that they can release a patch to fix the issue.
I have a LaCie 3TB Thunderbolt drive arriving tomorrow that I will see if I have the same ejection issues. That will help tell me if it's OS X (if the LaCie randomly ejects/sleeps as well) or if it's the Ministration (the LaCie is stable).
It's an annoying issue for sure, and can not be operating as intended.