iCloud path differences

My computer seems to have two paths to files on iCloud. And depending on how I access them sometimes the file opens to an empty file or a script complains the file does not exist.

The normal path

~/Documents/…/2024.09.17.gpx

in some cases opens an empty file.

But the other path seen is

~/Library/Mobile Documents/com~apple~CloudDocs/Documents/…/2024.09.17.gpx

Some apps and scripts don't work because of this.

Is this new with Sequoia and is there a way to tell apps, Terminal and Ruby scripts how to deal with this?

I previously posted about this iCloud files craziness - Apple Community

but the title may not have been the most descriptive. But the post includes other information