He hasn't really lost them, he just isn't in the same situations as he was. When he first came into the league, the league was just coming off a lockout and the first couple years had elevated PP rates. In 2005-06 Phaneuf was averaging 5:19 on the PP per game. He scored 20 goals that season and 16 of them were on the PP. The next season he averaged 5:34 of PP time/game and scored 17 goals, 13 of which were on the PP. Same thing in 07-8 - 5:00 PP time/game, 17 goals, 10 on the PP. His goal totals fell the next season despite 5:00 PP time/game, but it's likely that was just variance in his SH% - unlucky if you will. By 09-10, he was down to almost 2:00 less/game on the PP. As a result, his shot totals were down as well - 82 game pace of just over 200 rather than the 230-270 totals he was hitting before.
In 10-11 he was on pace for 236 shots and in 11-12 he hit 202 shots. It's really in the past two seasons Carlyle has given Phaneuf the toughest minutes he's had in the league and his shot totals have taken a hit - last season he was on an 82 game pace of only ~150, and this season his pace so far is for ~120 shots. Last season he rode a high SH% (just like in other years it's been a bit lower) and was still on an 82 game pace for close to 50 points.
He's just being used as a more complete player now. I don't think it's a matter of the tools being there anymore - he's not getting the same opportunities and not being used in the same role, so his opportunities for offence will take a resulting hit.