Does upgrading from OS X Yosemite beta to OS X El Capitan delete data?

You can perform an update from OS X Yosemite to OS X El Capitan without losing data. However it is a beta and there is a chance for data loss and corruption in an case so I advise making a backup of your system before installing the beta.

I am slightly confused however as you mentioned it is a Yosemite beta. Yosemite is in public release so if you arent running that I can be sure what is going to happen. You shouldnt be running OS X Yosemite betas any longer with the exception of things like 10.10.4.

Thanks, it transefered without a problem, I was still running preview versions of Yosemitie, I updated to the newest one then installed El Capitan.

Yes the update sets back /etc/auto_master to default.

Yes it does!

Everything that was not out of the box in e.g. /usr is not going to be there after reboot.

Now, you might argue whether that's actually "data" in the sense of user data, but it broke my (and some other users apparently) LaTeX distribution.

M