The Reconcile window when opened takes focus and requires user interaction. If the window is indeed rendering off-screen and you can not interact with it then Moneydance would appear to have frozen.
Open Moneydance and call up the Reconcile window. (At this point Moneydance appears to have frozen.)
Use key-combo ALT-SPACEBAR (A small context menu may or may not appear at the edge of the monitor.)
Tap the letter M on your keyboard so as to invoke the 'Move' command.
Use the keyboards ARROW keys (likely the LEFT ARROW key) to hopefully move the orphaned window back on-screen.