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Once the tool path has been run on G54, it is shown as fully run on G55 despite the G55 position starting new.

Any way to make it reset for the second work offset? It's just hard to follow the tool path when the entire tool path is shown as run.

That would require a toolpath re-generation and that happens with the g-code loading.
So, it would be possible, but it would take about the same amount of time as if you just reload the g-code.