Thank you for your post.
Yes, the installer removes the previous application and several unmodified file, and replaces it with a new application and files.
A couple of other users had problems with installing the FileMaker Pro 10.3 updater, and those users were installing to a network driver rather than an internal drive.
Also, one user had FileMaker Pro 10.0v1 on the internal D: drive and installed it to the C: drive, leaving some extra files on the D: drive.
No other problems have been reported.
Is FileMaker Pro 10.0v1/v2 installed on the local C: drive?
It is possible that downloading the updater was damaged. Have you tried downloading another updater from our web site?
What occurs when you run the updater?
Any additional information may be helpful in determining a possible cause.