Permabad, Minion will remember ones you've downloaded through Minion. So just re-download them (it wont mess with your addon settings) and Minion will start to track the AddOn and should continue to remember it. AddOns are very small so it won't take much of your bandwidth either.
Thanks for posting your minion.xml, everything looks good and it looks like it is already keeping track of 8 AddOns you've downloaded through Minion.
Code:
<addon md5="5e5d4b9c9adfd59509a23d47690d1106" ui-version="0.11b" uid="333"/>
<addon md5="f367807b16f1c15119da476ef789d144" ui-version="v0.9" uid="283"/>
<addon md5="f932b241ff58703995f9f53348cb5de3" ui-version="1.0" uid="141"/>
<addon md5="a00c533422dbc5568279a16db47d95bb" ui-version="0.2.1" uid="268"/>
<addon md5="3c2ca5141df695a860aea92f7534a717" ui-version="0.1.2" uid="335"/>
<addon md5="4dbbe731013fbee9b2c09839a222e20c" ui-version="1.0.6" uid="337"/>
<addon md5="54a0f6b2f56cd164a685999fc85e3135" ui-version="Version 0.02 beta" uid="312"/>
<addon md5="1f27338ff33200e8e5f2e1d58aaa4193" ui-version="0.6.4" uid="128"/>
We do have major improvements coming to Minion soon on addon detection. To better detect addons that have been manually installed.