There is much more to lose than just the x bit. AmigaOS has eight protection bits and each file can have a comment. Linux has three bits and no comments. So you always lose information if you go through Linux. Additionally UAE does not know that you are accessing an Amiga partition, so it might well be UAE who removes the x bit because the files used by UAE are not executable on Linux.
You can mount a data partition on Linux to transfer downloaded lha files and such, but you should not mount your system partition on Linux.
You can rather use /dev/sdb as a hardfile in UAE. It's so much easier to access harddrives as files on Linux than on Windows for example, so why not use this feature. You might need to run UAE as superuser to get the required access, though.
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