I was running a normal phase method using a phenomenex prodigy silica (5um) column. My mobile phase consisted of 86.5/13/0.5 (chloroform/acetone/acetic acid). After the analysis, I mistakenly washed the column with 100% methanol instead of hexane. My question is whether or not the column is still good to use? If not, could someone explain to me what I did to the stationary phase/column to render it useless?

to determine if the MeOH wash killed the column, simply make a run with the analyte and chromatographic conditions found on the test report that came with the column. Measure the theoretical plates and compare to the original value. If you are within 5%, the column should still be OK. I believe MeOH will dissolve silica, which is why you want to avoid 100% MeOH.

Methanol dissolves silica? I don't think so. Your column should be fine. When switching back to your mobile phase make sure you use an intermediate solvent, such as isopropanol to flush the solvent if they are immiscible. One word of caution however, use a slow flow rate, perhaps 0.2 ml/min if your column is a 4.6mm ID. Keep an eye on the pressure and try to keep it less than 2000psi or so.

Since silica has a small solubility in methanol so your column may have been damaged. All you can do is re-equilibrate in in your mobil phase (this will take a long time) and try a injecting a standard. With luck everything will be back to normal, if not, its time for a new column.

I agree with the first anonymous. Chloroform and methanol are not miscible, chloroform and hexane are. I guess when you tried to wash the column the pressure would have risen sharply. This may or may not have damaged the packing. Solubility of silica in methanol was not your problem. As suggested, if you want to try to recover the column use an intermediate solvent such as IPA to remove the chloroform and methanol then switch to hexane if desired then back to chloroform. See http://www.chromatography.co.uk/TECHNIQS/Other/Miscibility.htm. Good luck.

Slight correction.... Chloroform and methanol are completely miscible - no problem. Tom - your comment surprised me, and I looked it up in your reference - you looked down the wrong column.
Methanol is not a bad ingredient in mobile phases, and it is also not terribly difficult to get rid off. Since you are using acetic acid in your mobile phase, you will have no trouble whatsoever to get back to equilibrium.
Silica can also be used in water or washed with water. If silica were terribly soluble in water, we would not have any sand on the beach.

Oops...Uwe is absolutely right.