After having a closer look at the code, it turned out it is not so easy to fix.
Either:

1. remember the error in the plugin and disable auto save for this document (i.e. keep a map of all documents and their auto save status)
2. change document_save_file() in Geany itself to use info bars instead of dialogs to circumvent the dialog-document-focus-steal circle
3. introduce a variant of the document_save_file() function to return FALSE as now but additionally a GError object to tell the caller about the error but do not any GUI interaction, so the caller can handle error all on its own

I consider only 3. as a serious solution when comparing cost and benefits.
Though I personally probably won't work on this.

As a quick'n'dirty workaround we could add some delay in the plugin when the focus-out auto save resulted in an error. This would not solve the problem at all but enables the user to close the file manually or just fix the underlying file save error.

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