That 20-10 reverse at the Stade de France was their 14th Top 14 loss of a topsy turvy season but it doesn't tell the whole story.
Stade have shown impressive mental strength and some devastating attacking rugby at times this term, as was demonstrated in their Challenge Cup quarter-final victory over Montpellier and last week's 50-point thrashing of Bayonne.
The former Heineken Cup runners up overturned a 16-0 deficit to reach the final four in Europe at the beginning of the month before bouncing back from defeat to Clermont by scoring a hatful of tries that dented Bayonne's chances of reaching the Top 14 Play-Offs.
And Phillips is keen to stress that, while Clermont may be favourites to reach the Amlin showpiece in Cardiff next month, Stade have more than enough talent and spirit in their ranks to topple any team on their day.
"It was a bit of a weird atmosphere in the changing room after the game against Montpellier because some people were a little bit disappointed. But I came in and thought, 'We're in the semi-final of a European competition against Clermont and one more win and we're in the final'," said Phillips.
"Credit to the guys, they came back well. We scored four tries to one, so there was still some flair there. But a win's a win. We took that and moved on.
"We were down on the scoreboard at half time but we knew that if we could keep the ball and work them a bit around the field, we could score.
"Max (Stade owner Max Guazzini) came in at half time and let rip. Whether that made the difference or not, I don't know. But there's a lot of characters in the side and, despite what everybody thinks, we're fairly together and fairly united.
"Make no bones about it, we would have been on suicide watch if we had lost to Montpellier. But we didn't. We're still in it and we've got Clermont in the semi-final at home and then we go up against Munster or Quins.
"It's all to play for for us. This side has got that ability and talent to win these one-off games. We need to keep it together and keep it going."
Unlike Heineken Cup regulars Stade, Phillips has plenty of Amlin Challenge Cup experience from his time with Newcastle.
The England Sevens wing has seen some massive changes in the tournament since leaving the Falcons in 2009 and he is convinced the Challenge Cup is in the best shape it has ever been in.
But the fact that Challenge Cup standards continue to improve simply means the size of the task facing Stade this week, and possibly in four weeks time, is tougher than ever.
Just like their hosts, Clermont are a team packed with Heineken Cup pedigree; a side who are used to gracing the continent's greatest stage. They will arrive in Paris having already beaten Heineken semi-finalists Leinster this season and Phillips knows Stade will have it far from easy come Friday night.
But the sheer magnitude of the match should be enough to bring out the best in Stade. Whereas defeat to Clermont on April 16 had no bearing on their Top 14 hopes, the rematch means absolutely everything as far as Stade's season is concerned.
"It's our sole opportunity for Heineken Cup rugby next season, and also for some silverware. For some boys leaving, and for those staying, this is the all-important game now," added Phillips, who has been named on the bench for the semi.
"The Challenge Cup is much, much better now. The Heineken Cup sides have come down and they're hungry for European success and Heineken Cup success.
"Whereas before you had the runners up coming through from the Challenge Cup groups, you've got the five best sides, the teams who have really performed well. Alongside side them some seriously competitive Heineken Cup sides. The fact that the likes of Clermont, Munster and ourselves are in it leads to big games and draws big crowds and that's what this game is all about.
"The new set up's great. It keeps this competition really challenging and really interesting. Clermont are a top quality side. Their league form is hit and miss and they'll be eyeing this as a way of guaranteeing Heineken Cup rugby as well. It's a hugely difficult game but we're confident that we can win it.
"It's imperative for this club to be back in the Heineken Cup. Whilst the Amlin Challenge Cup is a great tournament, this club merits being on the biggest European stage. With the huge pedigree and history it has, that's where it should be and that's where we want to aim."