I am having the same problem. Printing PLA, on the 2nd layer the part cooling fan goes to 100%, and the extruder temperature promptly drops 10-15C and is unable to sustain the target hot end temp. I noticed it because the I heard the extruder skipping steps starting on the 2nd layer. This was due to the extruder not being hot enough to melt the PLA fast enough for the printing speed being used (100mm/s Linear Advance).
I've never noticed this problem prior to upgrading from MK2.5 to MK2.5S this past weekend. I suspect this is a side-effect of the new part cooling fan shroud.
This needs to be addressed in the slicer settings (although right now there is no printer-based limits on cooling fan speed... it's all in filament setup).... and/or the part cooling shroud needs to be redesigned. I'm surprised this wasn't discovered during testing.
I can reproduce this manually with the extruder at 0.2mm Z height, hot end temp set to 215, and part cooling fan set to 255. Hot end cannot maintain 215. (Yes, I did PID calibration). If I raise the Z up to 2mm, then the hot end is able to maintain 215 (barely), and it seems to get easier the higher the Z axis is away from the print bed.
I've read others reporting the same problem in this forum. Some suggest using a silicone sock on the hot end. I don't have one of these available to test with.
I'm curious to know what Prusa's recommendation is. Has anyone contacted support about this yet?