I just increased the amount of simultaneously opened files by samba inserting 
the following line into the [global]-section of smb.conf.
"max open files = 10240"
After a restart I was able to copy the above mentioned project without an issue 
- but that's rather a workaround than a solution. The files should be properly 
closed.

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samba "Too many files are currently in use."
https://bugs.launchpad.net/bugs/462172
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