This is an issue with Eagle.
If you wish your schematic and layout to stay "in sync", it is necessary to make sure Eagle has both the schematic and layout associated with one another and in memory during the changes.
The way to fix your problem, is to use "undo" to get back to where your pcb and schematic are synchronised and correctly reflect one another. Then make your schematic changes, making sure that both the layout and schematic have windows open at the same time.
This is one of the big problems with Eagle. Other packages have the ability to not have both in memory at the same time, and create forward and back annotation files that make synchronization possible. Eagle just does not do this, and instead tells you to keep both windows open at the same time.
Sorry... but this is a bit "Gotcha" with Eagle.