Hi all, sorry so many are having this problem.
I reached out to the RStudio IDE team, who has helped folks diagnose this issue in the past. In their experience it's typically not a change to the IDE, and instead caused by another piece of software conflicting with RStudio's keyboard shortcuts. Here's an example of that, Pipe shortcut stops working (Win10)[SOLVED].
If this is the underlying cause of your pipe shortcut failing all-of-a-sudden, it would explain why changes to RStudio's shortcuts or reinstalling the IDE don't resolve the issue.
I would check to see if there was update to a commonly used piece of software caused it to take over our shortcuts.