I transferred all my *coin clients, including their databases, from Debian Linux to FreeBSD. They were all properly shut down. None of them would work until I removed the databases and started from scratch. Should the database files be transferable between different operating systems?
I have no idea. It would depend on how the database library is written. The blockchain files themselves are platform-agnostic: values are written in a screwy byte order and each client is responsible for converting that order to their internal format.
If I had to guess, I'd expect the database files to be similar, and thus be compatible between operating systems, and maybe even between CPUs. But I don't really know.
When you say they were shut down properly, do you mean the databases were detached too? Do the altcoins even support that correctly?