After hours of research, I could not figure how to fix this issue. Here is what I have tried:
Step 1 Create backup copy of original FLA file
Step 2 Rename FILENAME.fla to FILENAME.zip
Step 3 Unzip FILENAME.zip
Then there are multiple things I have done after this:
Step 4 Open and copy contents of DOMDocument.xml
Step 5 Validate the contents at http://validator.w3.org/#validate_by_input
Step 6 Fix any erros excluding warnings.
Step 7 Check if error fixed by opening FILENAME.xfl
There weren't any errors so the DOMDocument.xml wasn't the problem and then I moved on to look for something else to do which I ran into something similar except this time to check the library:
Step 4 Open LIBRARY
Step 5 Backup and delete a few files or folders
Step 6 Check if error message changed from 'One or more files were not uploaded.'
Repeat step 5-6 until narrowed down to one file.
Step 7 Validate the contents at http://validator.w3.org/#validate_by_input
Step 8 Fix any erros excluding warnings.
But then the file that was cuasing the problem wasn't an XML file. It was a file that didn't neccesary have an extension and was named 'img.logo1' which was what I named it in the library.
I have only used CS5 and my file has never touched CS4.
This possibly may have been cuased by an update.
After an amazing epiphany, I finally found the solution.
Using the second method that I stated, I went through and found the file that I deleted.
After finding out that it didn't fix the problem, I looked for a seperate method.
What I didn't consider was:
What if more than one file got corrupted?
So I deleted the corrupted file and continued until I found another corrupted file.
After deleting the second one, everything ran perfectly fine after finishing the rest of the steps.
The only downside was that I lost the two files that I deleted which is nothing compared to starting the complete project over.