When any of your ships are outside of your range denoted by the thin grey line, they can still move back to an area that is in your range. In short, command it to come back close to home and it will. It won't explore fight or anything on the way, but you'll have full control again when it is back in range.

This also works if you end up with areas under your control that are far apart, ships can cross the void without the needed support if they end up close enough to one of your starbases or planets. Researching life support gives all your ships a boost in range, and equipping more support modules increases it for that particular ship so you might notice the line move when different ships are selected.

You select with a left click and the right click the destination, unless you have done something to your mouse like set to southpaw mode. Are you a southpaw? These instructions apply if you have system defaults set up...

You should either be able to left click on the survey ship or press tab until it selects it itself, then simply RIGHT click somewhere near your home planet and she will head on home.

I find sometimes having it set to auto survey or explore will cause it to go screwy; when that's the case I simply turn them off and set the destination to someplace inside the range border.