Ok so I got owned by a lvl 122 sara mage, died, lost loads of stuff.

I have the sextant and the watch. But I talk to the observatory people and I cant get the navigation chart back... Ive checked my bank for it and its not in there..

Any ideas?

I think you have to have a coordinate clue in your inventory in order to get a chart from the observatory people. Once you do you can get multiple charts by getting one, dropping it, getting another, etc, then picking them all up.