Firstly you asked how to fix the broken links, assuming there are any, editing the files is the last resort. To avoid broken links do the renames in two steps:
You should do it in these steps:
Rename the board and Forward Annotate to Expedition, exit Expedition and save. Now rename the schematic to Experiment - then forward annotate to PCB - once more - you will get the warning about missing root schematic - FA will fix this.