Seamless repeating pattern - using embedded images with clipping masks

Hi forum,
We struggle a bit creating a seemless repeating pattern that includes embedded images with clipping masks applied.
Our pattern is a 550x550mm black square with various embedded inserted on top. All of these images have Clipping Masks applied to hide unwanted areas.
These images are placed so they create a seamless repeating pattern and this includes areas that overlap the square.
Once we create a swatch from this pattern the repeatable area becomes too big as it includes the unwanted areas hidden by the clipping masks.
Because the repeatable area is now too big it's actually not repeatable.
We tried various things in order to solve this issue. Pathfinder/crop to delete the unwanted areas in the images etc.
None of them worked good enough.
We though of just livetracing the images, but due to the complexity this is not an option.
Do we really have to do our "cutting" in Photoshop or do you know any fancy tricks for issues like this?
Appreaciate your insight
Kenneth

Kenneth,
You may try the destructive deed, with the Clipping Mask selected:
1) In the Transparency palette/panel dropdown list select anything but Normal (Multiply is fine),
2) Object>Flatten Transparency, just keep the defaults including 100% Vector,
3) Shudder.
This should reduce the size to the Bounding Box of the Clipping Path.

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