The Ineos Grenadiers co-leader lost contact with the group of favourites on one of the climbs during a tough stage seven from Vierzon to Le Creusot, but managed to fight his way back.
After finishing with the general classification group, Thomas was concerned about the upcoming alpine stages this weekend.
Thomas, winner of the 2018 Tour de France, said: “I’m suffering, but hopefully I start to feel better soon. Or maybe not with the next two days…”
The Welshman has been suffering from the lingering effects of a crash early on stage three, when he went down and suffered a dislocated shoulder.
Thomas’s race looked like it could be over in the immediate aftermath of the crash, before a race doctor popped his collarbone back into place, with Thomas able to continue.
While he has pressed on despite the pain in his shoulder, Thomas battled through the stage five time trial to minimise his losses.
On stage seven, Thomas was briefly dropped on the penultimate climb of the day, Signal d’Uchon, before he was able to pace his way back onto the group containing race favourite Tadej Pogačar (UAE Team Emirates).
Meanwhile Primož Roglič, Pogačar’s biggest rival before the race, was also dropped on the climb but wasn’t able to catch the group, eventually losing around four minutes.
Roglič (Jumbo-Visma) has also been suffering with injuries he suffered in his own crash on stage three.
On his own crash, Thomas said: “I didn’t want to go 100 per cent. I was still in contact with 200m to go, so I just tried to pace it. I came back and it was okay in the end.
“It was quite a big crash and it’s easy to say ‘it’s okay’ but It takes a lot out of you, as you can see with Roglič. I didn’t want to go 100 per cent, I was still in contact with 200m to go, so I just tried to pace it. I came back and it was okay in the end.”
Thomas now sits 13th overall, 5-29 behind race leader Mathieu van der Poel (Alpecin-Fenix) and around 1-45 behind Tadej Pogačar.
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