Eclipse has a java implementation of svn, it probably has a compatibility problem with the eclipse kernel or with your command line svn client.
I suggest you transfer these files from the command line and then re-create your project from svn. Or create a backup of unsupported files, delete them from your project, make a full fix of the updates, copy the files and restart the update.
Eclipse has more svn packages (a pure java implementation and a wrapper for the svn library in C), for a long-term solution, I suggest you switch to another one.
You still need to check if your svn metadata format is compatible in your eclipse and your svn command line. He often changes silence.
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