Without seeing an example of your art, our ability to help is very limited. We need to know how these strokes are custom:
profile, brush, dashed, endcaps, etc
Try object >> expand appearance instead
You can also do a test by adding a live effect effect >> path >> outline stroke You can then run for example simplify, adn that an clean up what illuistrator is not liking. The live effect wil help you preview before you expand.