A few thoughts:
1. Flush any buffer salts out of your system with equal proportions of unbuffered solvent (if you were using 50:50 water:methanol with an acetate buffer, rinse the system with just 50:50 water:methanol), then with pure solvent (methanol after 50:50 water:methanol), then isopropanol, then whatever you're going to use for normal phase.
2. Find out if your seals and instrument are ok to use with normal phase solvents. Some instrument manufacturers sell seals specifically for normal phase (Agilent sells polyethylene seals for normal phase for the 1100 series). Make sure your detection scheme will work with normal phase solvents - make sure they won't damage the detector or interfere with detection. Get rid of any PEEK tubing, as it may swell or burst with the use of some non-polar solvents.
3. Make sure the column you are going to use has been stored in solvents that are miscible with the solvents you have on your system. If it has not been, then flush it with the appropriate solvent system before installing it in a normal phase HPLC (the same suggestions for flushing the system above apply to flushing the column).