I was recently migrating from Ecobee 3 to Ecobee 4. The installation itself was smooth (albeit I had to change both the furnace C-wire kit and the thermostat base, as they are not compatible between Ecobee 3 and 4). However, when I finished installation and added the new thermostat with to my account, Ecobee 3 data was not accessible any longer). The easiest thing to do, is to downloaded all your data just before you replace the thermostat. But sadly, I forgot to do that.
When I logged in through the web browser my Ecobee3 data was not there any more. I spoke to an Ecobee employee and he was very helpful. All that i needed was a 24V DC power supply. This is how you do it: Connect the power supply to Rc and C terminals. Slap the thermostat to the backplate. Wait for a few minutes and your thermostat should be online. It took a while before it appeared on the Ecobee web portal. Once it is available the data can be downloaded.
It is frustrating that Ecobee ties the data to the individual thermostat unit rather than the user account. If it were tied to my account, then upgrading should not cause any issue with old data. Hope Ecobee considers that.
Also, remember that you have access to download only the last 12 months of data. So, it is is a good idea to periodically download all your data.