We exported a single project and imported on target. I have randomly checked some warn messages in the log and found one filter was failed to import. I checked the xml and found the project in JQL is not related to the imported project.
The error "com.atlassian.jira.jql.parser.JqlParseException" means that parsing the JQL query for the filter failed. The best approach in these cases is copying the filter JQL query string from the XML file, and paste it into the JQL window at the target instance and see the reported error. This should give enough information about the nature of the problem.
About the last question in your comment, there is an option that includes in the export only the filters (or dashboards) that have been shared with any of the exported projects. That should serve the purpose of exporting only project specific filters.
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