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We've increased the calls limitation to 25 items per minute, and you can remove multiple tags from an item in a single call. However, we currently have no plans in supprting a flow of removing and re-applying all tags repeatedly.
A different way to solve this might be using the Scanner API to get the tags applied on all items and compare them with the tags applied on your 3rd party app, then using the delete/apply APIs only to apply the necessary diffs.