The space-weather phenomenon that is most likely to damage GPS satellites is spacecraft charging, a build-up of very high voltages within the spacecraft due to differential charging by high-energy particules. These voltage differences can result in sudden discharges, much like a lightning bolt, inside the spacecraft. Problem is that this seems to be more of a problem for satellites in lower orbits than GPS. It remains to be seen whether or not this will be a major problem for GPS, even in a large geomagnetic disturbance such as the one that followed the 1859 flare.

A more subtle impact might be small changes in the GPS orbits due to changes in drag on the satellite by increased local particle density should the shock from the CME push the magnetosphere in far enough to put the GPS satellites outside the magnetosphere and into the solar wind. These changes will result in short-term GPS errors, as the satellites won't be where they are expected to be. This, however, can be fixed fairly quickly by correcting the orbits and the orbit elements from which the expected positions are calculated.

I've been in the business of what's become known as "space weather" since 1972 (yeah, an Old Guy). One thing I've learned in this time is to ignore NASA when it comes to space weather issues. We in the community have been aware of this issue for decades, and it has been brought to the attention of The Decision Makers on many occasions at many levels with both government and commercial organizations. The lack of "leaping into action" has been stultifying, mainly because this disaster has never happened and so the bureaucratic take is that it can be safely ignored (same thinking that won't put a stoplight at an intersection until 10 people have died there). Recall that NASA is also the source of the lowest of the predictions for the upcoming solar cycle. So, on one hand they say "hey, the sky is going to fall" and on the other "hey, rainshowers at worst". All NASA cares about is publicity. The official organization for making these kinds of predictions is the NOAA Space Weather Prediction Center (I don't work there, or for them).

Shaky argument "we've already spent X, so that's lost if we don't spend more". The "sunk cost" argument, which is misleading. That money isn't lost, it paid salaries and bought some hardware that might find life in other programs. The question is, does it make sense to continue to pour money into this pot or would that money be better spent elsewhere. Knowing NASA and university operations, I'd suspect there are better places for the money.