I've seen Claude ignore important parts of skills/agent files multiple times. I was running a clean up SKILL.md on a hundred markdown files, manually in small groups of 5, and about half the time it listened and ran the skill as written. The other half it would start trying to understand the codebase looking for markdown stuff for 2min, for no good reason, before reverting back to what the skill said.
LLMs are far from consistent.
Try this: Keep your CLAUDE.md as simple as possible, disable skills, and request Opus to start a subagent for each of the files and process at most 10 at a time (so you don't get rate limited) and give it the instructions in the skill for whatever processing you're doing to the markdowns as a prompt, see if that helps.
https://scottspence.com/posts/measuring-claude-code-skill-ac...
This works in my experience
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