How do I force a new module to inherit the file permissions the modules directory has, after update?
I know this is old but recently I stumble upon the same problem:


Site installed on IIS 8 under Windows Server 2012 R2
After updating with Drush core and modules, permissions of modules
and updated files get messed up.


Solution I found is:


right click on website folder> Security > Advanced
check: "Replace all child object permission entries with inheritable
permission entries from this object"
Apply


If files don't shows navigate to /sites/default/files or whenever files are stored and change permission to this folder and subfolders.