Sadly, sometimes these limits may be slowing our bulk edits or imports/exports down.
Since this threshold is produced by Shopify, Metafields Guru team can't help that.
However, there are two options available to speed up the process:
1) you can contact Shopify Support team to explain the reasons and ask them to increase the limits for your store;
2) in case you're using a development or a trial shop, you may want to consider upgrading to a paid plan as those feature significantly some higher API calls limits.
Also, don't worry about the data being edited or imported as the API calls limit influence only the speed of the data import/export but not the quality.