A few people have had problems with their Macs when using multiple monitors, where windows that were put on secondary displays seem to disappear when the display is disconnected. The problem may happen more prevalently in certain setups where the computer is put to sleep and then the monitor is disconnected, but may also happen in other situations as well. Applications should reset their window placement when they are relaunched or when a display configuration is changed, but this may not always automatically occur. However, there are several things you can do to reposition missing windows.
One MacFixIt reader "Kate" wrote in to describe her approach for fixing this issues:
After updating to 10.6.3, I found that all movies I opened in iTunes were opening on a second display I was no longer connected to. I could view the film by choosing Full Screen view (Command+F), but there was no moving the window back from the phantom display to the primary display...I plugged in the second display, opened a movie on iTunes, and sure enough it popped up on the second display. I then dragged the movie window back to the primary display BEFORE unplugging the second display. Ta-da! All my films now open right where they should.
Many times applications will store window positioning information in application's preference files or in saved documents, so repositioning the windows manually before changing the display setup is one approach; however, you should not have to do this every time you want to change configurations.
An alternative way to fix this problem is to open the affected application and then go to the "Displays" system preferences and click the "Detect Displays" button (this can also be found in the Displays system menu for convenience if it is enabled). Clicking this button should trigger the computer to use only the connected displays and consolidate all open windows onto the newly detected desktop area. If the button does not seem to have an effect, temporarily change the display resolution and revert it back, which should have the same effect.
If the system still detects an external display even if one is not attached, first be sure all displays are unplugged when detecting or changing, and then restart the computer (optionally resetting the PRAM, SMC, and booting into Safe Mode) with the displays unplugged to see if that clears the issue.
Keep in mind that windows may still appear to be out of sight after being rearranged this way since the system may wedge them in a corner or against the edge of the screen with only a few pixels of the window showing. Additionally, the Dock may be covering a window if it was placed under it during the automatic rearrangement, so try hiding the Dock to expose an area of the window for movement.
Finally, as one additional option you can use Expose and Spaces to locate and move "lost" windows to a working desktop area. Invoke spaces and activate Expose at the same time, and you should see all open windows on all available desktops, and be able to drag any from one desktop to another. If an extended desktop is being used even though a monitor is not active or connected, then you can use this to locate windows on that desktop and move them where you can use them.
Update: While a "Gather Windows" button may be available in the system preferences for multiple-monitor setups, if windows are missing and the system does not detect multiple monitors attached then this option will not be available. Nevertheless, if it is present then it should also help locate missing windows.