If you want to transfer a whole project into a completely other JIRA instance and by that you want to remove JIRA Agile custom fields from the project, due to different custom field IDs this is impossible using import project function.
But there are two options anyway:
1. Simply – disable JIRA Agile and continue with the import
2. Or you can unlock fields and delete them, but JIRA Agile will lose info and will stop working at all – Instruction
Hope you found it useful!