Apple - packages installed with Homebrew not found after restore

From your answer above, it looks like you want to relink all your kegs, which is already answered here:

Is there a quick way to relink my homebrew kegs?

In one line:

brew list -1 | while read line; do brew unlink $line; brew link $line; done

It is documented that Homebrew fails after TimeMachine recovery a on a new Mac or making a Migration as Homebrew builds binaries for your specific machine: https://github.com/Homebrew/brew/issues/583

The official solution is to uninstall and reinstall homebrew. Don´t cry it's very easy with this line that remove and restore again all your 'formulae'

brew bundle dump && brew uninstall --force $(brew list); brew bundle