With regard to your ticket to support,
Please re-submit a ticket with more detailed information, if you were absent for a long period of time the accounts items would of been put into storage, Nothing can happen from the server side to alter the ship tree line or crews, this can only be done via access to your account.
Reply via support stating more information regarding the last time you played your account when the missing items/QE line were present.
If this was not too long ago we may be able to view trades from your account.
Reading the ticket it is most likely that another person with access to your account has utilized a BO Reset and maybe traded crews too and from your account.
If this is the case TNF/SDE do not support accounts that are shared.
Hope this clears it up for you