My idea is to erase the hole and redo them with a merge of the hole.

- separate the surface to have simple surfaces
- erase the edges of the hole to erase the hole on main surface.
- redo a closed curve with the rest of the hole under surface with small parts of edges.
- copy/paste this curve to have a closed curve extracted.
- Next reconstruct or rebuid curve to have a clean curve.
- extrude both side
- merge the extrude and main surface before cleaning and make a filet.

The result is pretty clean.

Next redo N-times or make a array of holes on a curve

right idea or wrong one ?

It depends on the final result needed. Extrem precision of the source for product ? Or a very near copy ?