The solution that worked for me is the following one given by Steve Hansen Smythe. I am just pasting it here. Thanks Steve.
"I found another scenario in which the red exclamation mark might appear. I copied a directory from one project to another. This directory included a hidden .svn directory (the original project had been committed to version control). When I checked my new project into SVN, the copied directory still contained the old SVN information, incorrectly identifying itself as an element in its original project.
I discovered the problem by looking at the Properties for the directory, selecting SVN Info, and reviewing the Resource URL. I fixed the problem by deleting the hidden .svn directory for my copied directory and refreshing my project. The red exclamation mark disappeared, and I was able to check in the directory and its contents correctly."