When I open Emacs to edit a Python project, the first command I run is pyvenv-activate to activate the virtualenv.If I have a Python file open for that project before running pyvenv-activate, flycheck won’t work because I install my development dependencies (which are needed by the checkers) in the local virtualenv.

Luckily pyvenv provides a hook that runs whenever a virtualenv was activated.

(defun clear-flycheck-auto-disabled-checkers ()
  "Clears any automatically disabled flycheck checkers."
  (setq flycheck--automatically-disabled-checkers nil)
  (message "Cleared all disabled flycheck checkers")
  (flycheck-mode)
  (flycheck-mode))
(setq pyvenv-post-activate-hooks
  (list (lambda () (clear-flycheck-auto-disabled-checkers))))