Safari in 10.10.4 completely non-functional after simple preferences change
I wouldn't expect reinstalling the system using the Recovery HD to cause any significant problems. Minor things that come to mind are reinstallation of fonts in /Library/Fonts if they'd been previously removed, and the possibility of needing to reactivate copy-protected software, e.g. reentering the Microsoft Office serial number. But you've no doubt faced these same issues with the previous upgrades.

You could do a trial run without making any changes to your system:


Use Carbon Copy Cloner to clone your boot drive to a new or empty external drive.
Reinstall OS X on the cloned drive.
If things look good, reinstall on the original drive, or clone back.