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I just want to make sure i understand. If i use this on a animation with multiple layers under it, there will be issues?

There should be no issues, the best way to import animation from a file with multiple layers is to import by tag - all visible layers are merged in this case.

In comparison importing by layer takes only the image from a selected layer, regardless of whether the layer itself is visible. And importing a selection from another file takes the chosen part of the active cel (cel is the selected frame of the selected layer).