Not sure if I understand exactly what you try to accomplish but what you want to do is probably not a simple thing. It's very doable but there are some pitfalls and if you try to do it all in one go it might even be hard.

Multiple ways to do this, but my strategy would be:

• Create a process to scan the directory/directories and create a to-do list.
  • The Directory and File Pathnames can be used to directories and list files / folders.
  • I prefer a database table for the to-do list, because then I can see the progress while FME works on it. Anything that won't lock the file for writing while watching it, which is happening with file based formats as Excel. I often use PostGIS or SDE because I have these at my disposal but there are a lot of alternatives.
• Create a process to read the to-do list, process a file from the list and update the list when processing is ready.
  • These are actually two workspaces, a parent (reading the to-do list) and a child (processing a row from the to-do list). The parent contains a WorkspaceRunner to start a child for each file.
  • This way you can process one file at a time, which helps with performance (not having to read all files at runtime which eats RAM) and allow you to pause or stop and later continue the processing when something fails. (Not if, when.)
  • Use FeatureWriters instead of classic writers. Then you can chain another writer after writing is done, updating the to-do list.

A tool that we've had success with when dealing with LAS files is LASTools - https://rapidlasso.com/lastools/

We've integrated it pretty heavily with FME into a number of our internal workflows. There's a few custom transformers on the FME Hub for it, if they don't do what you need, the documentation is pretty detailed and has lots of examples.