Do you know how to accomplish a chmod in Linux?
Here’s a breakdown if you need to learn: https://www.howtogeek.com/437958/how-to-use-the-chmod-command-on-linux/
From your description, it looks like there is read write permission for the user, but no group or general permissions. Again, I don’t know if this will work, but it is where I would start.
Open your terminal and type:
sudo chmod 777 /path/to/file.txt
That will allow all users, groups, and guests to read, write, and/or execute the file. Then, if your programs are set to run under their own user or group, this will open the door for them to be able to access the full file.
Other than that, I’m wondering if the original file names have a structure that one of the systems can’t handle (such as slash marks) and so it changes the name to accommodate.
This is going to take some trial and error in troubleshooting. If you aren’t familiar with your terminal yet, this is going to be a great learning opportunity. Just make a backup of your files and system so you can undo any mistakes.
Did you run it as sudo? And you’re on Ubuntu?