R2 is a navigation droid, so presumably keeps a record of everywhere he’s been for audit trail purposes. He’s also (up until that point) never been memory wiped unlike C3P0, so having part of that route erased is a big change from previous canon.

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The map in Ahsoka isn’t necessarily a map to Thrawn specifically, someone else mentioned it being a map of migration patterns but equally it was mentioned in the episode that some beings travelled from another galaxy to the main Star Wars galaxy in the past. Morgan may just be assuming that’s where Thrawn was taken by the purrgil as they roam all over, so the map may be a bit of both migration patterns and a record of where the travellers came from.