Hello, and sorry for the inconvenience. As part of the Mega Man 4 update, the mission structure was completely recoded and every player had their progress reset to the beginning. It is unfortunate that I had to do this, but it was necessary for the new content to work properly.
Because everyone is playing a (very clearly stated) work-in-progress, you're basically all beta testers and as such your experience may not be perfect. :| This style of development is obviously not perfect and has its flaws, but it also has a lot of good aspects too - you guys get to play and beta-test years earlier than you would otherwise and we get real-time feedback when we implement new features.
That being said, your robots have not been reset and your abilities should all be there too. Your Level 100 Mega Man alone should make playing through the new missions a breeze! :P