I understand the existing waveguide was for VHF 11, which is where they are digitally, not UHF 47. You're correct that it won't work for UHF 49, which is where they are going digitally.
Yes, the
active feed line* carries the 201 MHz VHF signal to the currently active antenna. However before the change to ATSC, the NTSC station WMSN-TV was broadcast on UHF channel 47 at 668 MHz. Hence the station name "Fox 47" and PSIP designator of 47. The waveguide for the old "channel 47" was not torn down, even though it was no longer used. When the station was awarded the 680 MHz frequency (which matches the obsolete NTSC channel 49), they had hoped that they could re-use the old waveguide, the rationale being that the frequencies were close enough that they could "make it fit". To make a long story short, they couldn't. So, because of this, a new waveguide tuned to what we used to call "channel 49" is being installed.
When that goes live, the PSIP tag will remind your tuner that ATSC station 47.1, 47.2 etc is at 680 MHz now. When the change is made, we will need to re-scan our ATSC receivers to find the new PSIP so that when you "tune" to Fox 47, you will get Fox 47 on its new frequency.
*I doubt that a waveguide is used at 201 MHz. It's generally not practical at VHF frequencies due to size and weight constraints. Remember that the size of the wavelength is inversely proportional to the frequency. At VHF frequencies it's more economical to use less efficient coaxial cable with more raw transmitter power to make up for cable losses, than it is to build a new, gigantic tower capable of supporting a VHF waveguide safely.