I don't have the actual confirmation for you on this as I too took outposts undetected. However I did run into another problem concerning the outposts. My supply trucks stopped running when I liberated all the outposts. Resetting all the outposts fixed that issue for me so when you reset them there are more effects being reset. So hopefully the ability to take an outpost undetected will reset for you too.
Thanks again for all the comments. Just to confirm a couple of things (I have tested this):
1) Resetting the outposts and then liverating them stealthily does count towards the perks.
2) Resetting the outposts does put supply trucks back on the roads so you can hijack them.
Pretty much been said already, but there's confirmation.