As the title says, I went to send a couple of messages and I saw Thunderbird being removed in real time, without a warning.
A few moments of panic, then I noticed it also installed a different version… crisis averted 
We cannot touch the installed flatpaks once they are installed, even if we would remove something from the default flatpaks that get installed when the OS is installed.
I’m curious, was this Flatpak related or a change in the underlying system?
Thunderbird made a recent change in their flatpak, I suspect it was from that. Thunderbird has always had the ESR release on flathub, and it it was very behind on features from the latest Thunderbird. In the last week they transitioned org.mozilla.Thunderbird to org.mozilla.thunderbird-esr. I think when he updated it transitioned him from org.mozilla.Thunderbird (capital T) to org.mozilla.thunderbird (lower case T) which is the recent new latest Thunderbird they just added this month. In doing so it likely told him the previous ESR version was being uninstalled.
Gotcha. Thanks.