When you choose to build packages from AUR you need to know that every time you update your Manjaro system - there is a chance that your AUR packages will need rebuild and therefore - when an AUR package acts weird after an update - rebuilding said package is often the solution.
You cannot - and most importantly you should not as it will cause irreparable damage to your system files.
Manjaro repos is drawn from Arch and synced several times a day from Arch stable.
Except from some obvious packages like kernels, kernel modules, nvidia drivers, a few Arch specific packages (e.g. arch-install-scripts) and Manjaro specific applications - there is nothing in the Arch repo which is not available in Manjaro repo.