If I am understanding your question correctly - you sew pieces together - and then decide to "subcut" - ??
You could sew your seams with a backstich -
google: back stitching in hand sewing -
That is a seam that is very durable - and quite a challenge to remove! - but it would survive - up to a point - your units being cut apart without falling apart as easily as when one uses a running stitch.