Open Manage | External Data Sources...
You'll find a list there of all links to files outside your current one. You can examine and edit these links to correct that problem.
With regards to file size. I have several files here that exceed a GB and have over 100,000 records. While there isn't an issue with filemaker that will corrupt your data as the file becomes large, repairing any corruption that exists becomes much more time consuming. File corruption is not normally the cause of what you are reporting here so I wouldn't worry about that unless you see other problems such as
Sorts that don't sort correctly
Finds that don't find the records expected.
Then you may need to revert to a back up copy or recover your file (may take a long time) and then import the recovered data into an undamaged clone of the file.