You have been here for more than two years and yet you don’t provide any information of what version you are using and therefore you will not get the best possible answer!
Depending af how far you got in the salesprocess and NAV version there are several solutions. IF you have shipped but not invoiced then on new versions of NAV you can undo it - but on older versions you cannot. On older versions you have two options - either you do a line with negative Quantity and a new line with positive Quantity to fix it, or you fully invoice the customer, make a creditmemo and a new order again.
A good old NAV 2009 R2. EIther Create a nev negative line in the order(and post the SHIP of it, and a new positive quantity line) Depending of the Exact build you could also try to if Shipped is lets say 2 try to post -2 in ship and see if that works. The best solution is though to create two new lines.
The beaty with NAV is that it has been envolving with rapid speed. So from one version to another a lot of stuff is changing, and therefore a NAV version is necessary.