I just thought I would chime in that I have had this happen a few times when moving the unit, and twice when the unit was not moved one bit, so keeping a BM CD handy is a good idea. It always goes back to working, but it can be a pain.
most people report that it happens when moving the PS2 around
If your memory cards are highly configured what you could do is back them up to folders on your hard drive using uLaunchElf so that if you have to clear them you could restore them quickly and easily. Jones23 knows the proper procedure for that. I think it involves using Psupaste or MCPaste, I can't remember. One of those functions within ULE guarantees proper integrity of the memory card contents. It would be a nice thing to look into in case you have to restore your cards. CC 2.0 users usually don't have this issue since BM is on the on board flash, but I can see where it would be a hassle for your setup.
Also I just thought of something else. A time or two I have just copied the contents of one memory card to another for backup purposes. You could get a couple of spare memory cards and use them as backups so if this ever happens again you could just pop in the backup cards after flashing the firmware.
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