I've manually run a Thunderbird update using a new 64-bit version. As I already have a 32-bit version installed, the update went into the C:\Program Files (x86)\Mozilla Thunderbird folder.

This is expected/intended behavior, for reasons we don't need to go into. Neither Microsoft nor Thunderbird care that a 64bit program is in an "32bit" directory.

IConsecutive updates will change the version to a 32-bit version again.

No - future updates will be 64bit.

I don't copy the last sentence you write, as I have 2 installations that recently got downgraded to a 32-bit version.

But the problem might actually be not caused by Thunderbird itself, but by third party software we are using.

One of them is Ninite, I'll get in contact with them.

Indeed, third party software which manages updates might screw it up.