I think it's because of the .classpath getting saved with the deleted source folder configuration.
Create the missing folder [ 'src' in your case] manually inside the root of the project. When I say manually, I meant outside Eclipse, using the file explorer.
Then, come back to eclipse and refresh the project. Now, the error saying it's already there will be gone.
Now, Right click on the project > Build Path > Configure Build path. It should take us to the Java build path side menu.
Make sure we are on the 'Source' tab. Delete the source folder causing the problem. Now, maybe the folder might show up in the project structure and you may delete that too.
I was confused by this for hours.
Right click on project -> Build Path -> Configure Build Path -> Add Folder
If you are facing an error with the folder, such as src/test/java or src/test/resources, just do a right click on the folder and then create a a new folder with the name being src/test/java. This should solve your problem.
In my case eclipse reported this in the Problems view on the parent project which does not have any code. I just delete the error whenever it is reported on this parent project where src folder is really not needed.
Create the src folder in the project.
Right-Click Project --> Build Path --> Configure Build Path; unselect the SRC, save, select again.
This solved my problem.
In eclipse, you must be careful to create a "source folder" (File->New->Source Folder). This way, it's automatically on your classpath, and, more importantly, Eclipse knows that these are compilable files. It's picky that way.
Here's what worked for me: right click the project-> source -> format After that just drag and drop the source folder into eclipse under the project and select link.
good luck!
One of the build path issue is it cannot find the correct /src/conf source folder. Right click on each project, Build Path > Configure Build Path. Under the Source tab, remove the folder with a red cross icon on the bottom right. It will work for the situation that there is a small red exclamation mark “!“ bedore your project name!
Eclipse wouldn't let me point to an existing (or add a new) source directory. Eclipse's configuration files can be wonky. In my case I should have started simple. Right click the project and click Refresh.
Right Click Project -> New -> Folder -> Folder Name: src -> Finish
Edit your .classpath file. (Or via the project build path).
Right-Click Project --> Build Path --> Configure Build Path-->source-->(Select missing folder or path)-->Add Folder-->Apply-->Ok
Go to the Build Path dialog (right-click project > Build Path > Configure Build Path) and make sure you have the correct source folder listed, and make sure it exists.
The source folder is the one that holds your sources, usuglaly in the form: project/src/com/yourpackage/...
Source: Stackoverflow.com