Like I said, I updated an old project (6.1.2) and I saved it under 6.4.
I closed sh3d then I re-opened the project, the walls (not all) became unjoined...

Hum, it's not what I read [;)]

I just tried to reproduce your issue on a file created with version 6.1.2, but opening, saving and reopening it with version 6.4 didn't show any unjoined wall. There must be something else... [:(]
As the version 6.4 introduced more IDs on plan objects, I hope I didn't introduce a bug in the management of existing wall IDs.