So, it appears that the 2.2.2 update removed waypoints for some people, here's how to fix: If on ftb launcher and if you selected to back-up configs before updating to 2.2.2, then as follows: do an OS search for 'waypoints' to find the current folder (which should be empty), you should also find previous 'waypoints' folders, these should contain your saved 'points, copy/cut and paste and re-log/restart. Voila!
I've done a research in my OS, i've only found the waypoints of the map i have on my FTB launcher. No signs of the waypoints i have on Mym's servers and maps. Also i've found that all the waypoints o have on FTB are from JourneyMap., but on the mym servers i use Voxelmap. Maybe the waypoints are hidden in .class files
I've found the waypoint folder ".point", i've openned them and copy/past all my waypoints in the new one. folder in: <OS>\Users\<yourname>\AppData\Roaming\.mineyourmind\instances\MyM-<modpack>\minecraft\mods\VoxelMods\voxelMap I have now all my waypoints back on the right map =) thanks! I wish you all a good day =)