Since I didn't see the details posted anywhere I thought I'd let peeps know what happens if you opt to reset your Commander profile to regain lost Infamy points.
It looks like the points that get reset (meaning you need to earn them again) are mostly on the first tab. You keep any points for completing an operation with a specific House gang, but you lose all the points related to completing operations against gangs of certain point thresholds. You also lose the points related to raiding gang HQs.
Finally, the points you earn for hiring experienced gangers (I think there's 5 unlocks, worth 3 points each, all on their own separate tab) also get reset. But you can easily get those back by just hiring and retiring one experienced copy of each ganger type.
In conclusion, the reset tool works very well (I am no longer on minus 100 Infamy!), but after using it you will need to complete one Deadly operation, end it with the max/tier 3 reward, plus raid an enemy HQ to grab as much loot as possible. Not a huge issue really.
I'm not sure if the bug relating to raiding HQs is still in effect, so it might be harder than it was originally to gain the top points (i.e. for stealing 150 points worth of loot). I remember this was bugged when I raided my first enemy base and I got far more Infamy achievements unlocked than I deserved.
Hope this info helps some players