That error is happening when calibre is writing the file "metadata.calibre" to the root directory of the device. Most times I have heard of it is with lots of books on the device and the 32bit version of calibre. 5000 shouldn't be enough to trigger this, but, the file includes all the metadata in the library and is formatted with leading spaces. If you have a lot of custom columns, or a lot of text in the long text fields, it will be bigger.
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