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I feel like this is a simple answer and I kind of feel like I know the nuances between when to use the tool. I'm finding it hard to articulate in which use cases one is better than the other. Can anyone think of when would best to use append instead of join?
To use the Join tool, ideally you'll want to have a field in both datasets that match. Either an ID of some sort, or a combination of fields. The Join tool allows you to add data to your dataset only where it matches based on the common field.
There is an option within the Join tool to join on record position. This acts sort of like an append where the first record from each input is matched regardless of the data within it, however it will only match the records to the lowest record count from the Inputs. For example, if one input anchor has 100 records and the other has 1,000, only the first 100 records will Join using this method.
The Append Fields tool adds all of the information from the S input (Source) to the records in the T input (Target). If you're not careful, you can blow out your data into a huge dataset. If you have 100 records on the Source side that you are appending to 1,000 records on the Target side you will end up with 100,000 records because each of the 100 Source records gets added to each of the 1,000 Target records.
To help with this issue, there is a setting at the bottom of the configuration for the Append Fields tool allowing you to decide what to do if the append creates more than 16 records: Error, Warn, Allow All Appends.