My mouse and keyboard seem to "disappear" the next time I boot into a freshly upgraded version of Xorg on Gentoo without fail.
Xorg does an internal check that the OS doesn't (dynamic linker). They probably did this because they tend to do minute API changes that aren't ELF linkable (like saying passing a 2 means delete this window, and 1 means to create; and then the next version they swapped the meaning of the two arguments). This can't be detected by the OS (which is what revdep-rebuild does), so Xorg put some internal checks, made each binary have their own version to keep versions straight.
Quick fix if you're on generic evdev:
# emerge xorg-server xf86-input-evdev
One size fits all:
# emerge -1av $(qlist -IC x11-drivers/)