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Checked. It worked for me.

1. Open your 2layer patern file.

2. make sure they transparent and no white background.

3. make invisible 1 layer.

4. go Edit/Define Pattern. lets say my pattern1.

5. make invisible 2 layer and visible 1.

6. Edit/Define Pattern - my pattern 2.

Beware that your pattern have transporancy.

Now make your project file at your size with transparent layer 1 and layer 2 (or whatever names)

Fill it with my pattern 1 one of them and my pattern 2 other.

Must work.