Updating system caches mac os x
Note, download times may be longer than usual on first release.
Backup (link explains how) your data before you install anything.
The fact the update works at all is a testament to how well tested the software is.
As a result an update may appear on the surface to be bad, but in reality a contributing factor is causing your problem.
IMAP e-mail is by default server based, and if you trust your internet provider to back it up, may be a better solution.
Moving from POP to IMAP is something you have to do with care, since by default POP is based on storing everything on your Mac.
A similar flaw was corrected on i Phones, i Pad, i Pod Touch with the i OS updates below (i OS 5.x and earlier are unaffected).This means you'll have to rely on an Apple update that includes it to repair your permissions. There is a command line repair permissions option if you really need it.Apple released Security Update 2017-003 for El Capitan Yosemite was released 10/16/2014. Software tested before that date may or may not work at third party download sites.Just because you've seen an issue which appears on a bulletin board, or is reported to you by a friend in a Mac OS X update, it does not mean the update is itself bad.
A mathematical improbability exists to test all combinations of software and hardware compatible with Macs.You should really at least backup everything to two separate destinations that are not touched by the computer before upgrading or until after the upgrade is complete. Printer and scanner driver issues with Yosemite are covered with more details on my Mac OS X printers page.