Applications in a Debian .deb package repository archive file are cryptographically signed by the author(s) to ensure integrity even on public servers. This information can be loaded post installation to verify your local installed files are the same ones built and reviewed by the community. If you wish to check for file alterations, you may open a command line terminal with Ctrl+Alt+T to scan and repair the OS installation. Note, this process differs from a low level file-system disk-scan repair, and just checks if specific files were modified/corrupted/lost.  This trick is highly recommended if a program exhibits anomalous behavior even after a reboot.

1.) To scan your installed Operating System for modified files (after a disk-check completed) run: 

sudo debsums -sac

While /etc/config path files are often modified for some programs, ideally no modified binary applications or libraries should appear in the charged list. Sometimes local updates/workarounds are needed for bug fixes, but these customizations should be avoided if possible.

2.) For example, we can imagine the list detected a failed check of some arbitrary file: libqt5scintilla2.so.12

We would want to scan and list which packages the modified file belongs with by running:

dpkg --search 'libqt5scintilla2.so.12'

3.) If you see that indeed this file belongs to a package in your known repository, than we reinstall the package files by running:

sudo apt-get install --reinstall libqt5scintilla2-12v5

This method can often replace missing or corrupted files on a failing/damaged drive, but is usually only run if something unexpected is happening.