I experienced similar:
Mid-mission, I discovered several modules not activating with the error "module offline". (The visual readout still showed them as online btw)
I took the ship back to the nearest station, assuming they'd simply been switched off accidentally, and that there was a readout bug.
The fitting screen showed them as online.
I tried unfitting them, and then refitting them. This didn't work because somehow the ship thought the modules were still "there" (and draining power + cpu) just offline (it took me until I'd stripped everything off to work this out).
Tried undocking/redocking; Tried buying a shuttle, switching to that as active ship, then switching back; Tried switching to shuttle, undocking/redocking, switching back to my clone.
For my efforts I was left with a non-existant ship, with worse stats than a pod, and no station environment image.
To make matters worse, when I logged off, I became unable to access my main.
I was left unable to access my main, all evening, and when I checked in the morning. The problem only went away after the server downtime.
My advice if it happens to you:
Stip every module from your ship, pettition to make the gms aware of your problem, find a spare ship to fly, and wait patiently till the reset (with a stop by to check if your ship's better again every now and again).