I've been playing a career with Kerbal Alarm clock installed, so I left my probe going to Duna for it's long journery and in the meantime did a bunch of contract work.
After a while, the alarm goes off, I try to go to my probe to get it ready for it's insertion maneuvre, and low and behold it's vanished from existence. Next launch window isn't for over a year
Ohh that's not fun.
Did you do a lot of contract work that involved re-entries?
Because it sounds like a NAN error in your Persistence save.
ie, your Duna craft got a NAN error, induced by several launches and re-entry of other craft for contracts.
Once your Duna craft had a NAN bug, the observatory then deleted the craft.
I believe there was changes made to version 1.0 that will lower any further chances NAN bugs.
As for the DLC debate. I am not 100% positive.
But believe Squad has dropped the idea of Paid DLC.
They are committed to Develope and add new content/features for some time into the future.
For how long? I truthfully do not know.
After 1.0 is released.
Squad has plans for several more undisclosed features. Plus Multiplayer and more new content.
Bug fixs and balancing as always as well as unity 5.
And not all of those are planned for version 1.1.
Fear not Kerbalnaughts.
Squad knows it has a great community and following with KSP. They will continue to develop it, and expand.
But have no intention of fragmenting us, with Paid content.