reactivate second monitor in el capitan
This is a two part workaround:


an  applescript to click on the detect monitor
a bash script to run the script


I "saved" the applescript to $HOME/source/detectmonitor.scpt (see 
Run AppleScript from bash script) how to work around the issue that you can not really start with a text file ...

Then I saved the bashscript to $HOME/dm

I created a symbolic link
ln -s $HOME/Desktop/detectMonitors $HOME/bin/dm

and set my Terminal preferences according to https://stackoverflow.com/a/8822669/1497139

now i can double click "detectMonitors" on my Desktop to work around the issue.

Applescript to click "detect monitor" in monitor system preferences

see https://stackoverflow.com/questions/12640643/applescript-to-run-detect-displays

-- Script to click the "Detect Displays" button
-- 2015-12-22 WF
-- see https://stackoverflow.com/questions/12640643/applescript-to-run-detect-displays
-- adopt to your language settings by setting the right button name below
-- currently this is german "Monitore erkennen"
-- to create and run this script you need a compiled scpt file to begin with see
-- https://apple.stackexchange.com/questions/103621/run-applescript-from-bash-script
-- then you also need to set the security settings
tell application "System Preferences"
    activate
    reveal pane "com.apple.preference.displays"
end tell

delay 0.5

tell application "System Events"
    tell process "System Preferences"
        try --don't even consider not using a try block!
            key down option
            delay 0.5
            --click button "Detect Displays" of window 1
            click button "Monitore erkennen" of window 1
            delay 0.5
            key up option
            tell application "System Preferences"
                quit
            end tell
        on error errMsg --logging out is the only other way to clear these
            key up option
            display dialog "ERROR: " &amp; errMsg
        end try
    end tell
end tell


Bash-Script to run the applescript

#!/bin/bash
# WF 2015-12-22
# run detect monitors
cd $HOME/source/applescript
osascript detectmonitor.scpt
# set Terminal settings
# according to https://stackoverflow.com/a/8822669/1497139
# to get this to close your terminal window
exit 0