I had knee problems on one tour and just toughed it out, other than walking a lot of the harder climbs and taking walking breaks even on the flats when it felt especially bad. I figured that I had a torn meniscus and would probably need surgery when I got home, but didn't want to end the trip. I wound up being fine in a couple weeks. I can't say that I advise that approach, but it worked out well for me in that case. Taking some rest days is probably a smarter approach.

I can advice being sure that bike fit including saddle height and cleat position, especially cleat angle are dialed in. Very small differences in those settings matter. Also I hope you are running sufficiently low gears and not mashing a big gear up the climbs. That also makes a big difference.