Alternative to @scotthenderson's and @mattgraney's suggestion, which would work, you could potentially make this a bit more automated. This does assume that the global updates you are making are to fields that shouldn't every trigger the flow to send an update even if not mass updated. I had a similar use case at my last company where some fields would get updated daily, but those fields had no reason to trigger updates to external sources.
- First option could be to add search criteria to your saved search that filters on the system notes. You could filter out system notes where the field that changed is the one or ones you don't want to trigger this flow off of. You could also filter on context and filter out where your context is a csv upload or something else. If you do this, you also have to make sure to summarize the results of your search so you don't have duplicate results returned for each system note. This can be fairly detrimental to the saved search performance so you may also filter system notes datetime to just the past 24 hours or so.
- Second, you could create a beforeSubmit function or workflow on your item records that updates a custom timestamp field when certain things are updated or within certain contexts. From there, you could choose that timestamp on your delta export instead of native last modified date.
