Intellij has a lot of interesting features and for that it makes use of cache. That sometimes makes problems like this. After invalidating caches and restarting IntelliJ the dependencies that were cached are removed and updated on the next compiling, and these errors were fixed.
When writing to the file, I was using Writer. The solution is switching to OutputStream.
From JDOM reference, org.jdom2.output.XMLOutputter, output(Document doc, java.io.Writer out):
Warning: using your own Writer may cause the outputter's preferred character encoding to be ignored. If you use encodings other than UTF-8, we recommend using the method that takes an OutputStream instead.