I can't elaborate much more on the issue of AFE drives and generators, I just know that it's an issue. Aside from the one mfr that definitely says so in their manual, the other main player in that world will neither confirm nor deny it is a problem, but I have two customers that are having major issues with it. The drives work fine when on utility power, but when they run the backup generators (pump station), the drives just shut themselves down with no fault displayed. In one large pump station project installed last year, it has reportedly progressed to the point of calling lawyers because nobody is getting paid. I don't know what the technical issue is behind it however I do know that some new competitor's products due to be released next year are touting that they know what the issue is and have fixed it. We'll have to wait and see on that.
As to AHFs, yes, they are a better solution for multiple drives, large or small in my opinion. For AFE or 18 Pulse, you are buying a harmonic solution for EACH drive. With an AHF you are buying one unit that covers them all. I did a project last year with 4 x 400HP drives, the 6 pulse drives + an AHF cost about 30% less than the AFE drive solution. Then as it turned out, they would never run more than 2 pumps at a time, so we lowered the size of the AHF and saved them even more.
Cost wise, the issue with an AFE drive is that you are essentially buying two drives for every motor, because an AFE VFD is basically two back-to-back inverters. Yes, the front-end inverter is replacing the diode bridge, so from that standpoint the difference seems to be just the cost of transistors (and their firing circuits) vs. simple diode bridges, but there is more to it than that. Because an AFE drive is capable of putting regenerative energy BACK into the line, an AFE drive must add line loss sensing to so that it shuts down and doesn't kill a Linesman if the utility goes down. Also, there is a lot of necessary filtering that must be added because the transistors are more "delicate" when it comes to line disturbances. So the AFE drive must add line filtering, typically an LCI filter, so if you are not a fan of filters, you are adding a LOT of them. Those added protections result in the overall cost of the AFE drive being roughly 2X the cost of a standard drive.
Then from a reliability standpoint, an AFE adds a significant component count to each and every drive, so your MTBF (Mean Time Between Failures) drops significantly. I don't know what it is however, I just know it has to be lower because that's how the math works. And if the harmonic filter fails, you just don't have a harmonic filter. If an AFE drive fails, you don't have the drive.