Sorry for the result on your end, but just to reassure you, we had an extensive rehash of all the data in last years' CRM topic at my current base. We also did the same, with some great discussion at my previous squadron. Not sure where the disconnect is, but I felt confident that both of my squadrons were pretty extensively informed. Both reserve squadrons I might add, but the CRM classes had both active and Reserve dudes in it.
Just brought a tear to my eye. Everything up through the night before was the same, except I remember that the sequence of events was clearly, mask down, puke over side, mask up, start number two, taxi out, avoid new FOD.
Will not affect security clearance. Call the legal and P/A guys at your unit.
That being said, the hardest part of dealing with USERRA cases are the commitment of the employee to follow through with them (fear of retribution, future hostile work environment, etc.).
I've staved off a few potential issues with letters to employers - first a nice one.
Good luck on this.