When exporting to Acrobat Pro X from InDesign CS6, there are times when I want to overwrite an exising file but I get an error msg that the file is in use (it is not--this even happens when I have closed the file and quit Acrobat) or i don't have permission. In the Info panel at the Finder, i see that "myusername (ME)" does have permission to read and write this file. As a test, I also changed the permissions for Admin and Everyone to Read & Write, but that did not help. I've checked Preferences in both InDesign and Acrobat Pro anc can't find a relevant setting.
To save the file with the same filename as the pre-exisitng PDF, I have to close the pre-exisitng PDF and move it to the trash.
I have no problem overwriting a PDF document from Acrobat. This only happens when I am exporting from ID.
I am on a Mac running the latest version of OSX.
Have you run Disk Utility > Repair Disk just for good measure?
Make sure that the PDF you are trying to overwrite is not selected in your finder. I've found that if it's selected in the finder then the preview tricks Indesign into thinking the file is busy