/etc contains files involved in package management, so replacing these files with older versions may break respective software packages. Imagine you had
/etc/foo/config which contained a setting
bar=0 at the time you made your backup. Then a newer version of
foo is released where
bar was renamed to
baz. When you install this package,
/etc/foo/config is also updated to replace
baz. If you now restore the old backup,
foo will complain about an unknown configuration parameter
This gets much worse when security is at stake. For example, restoring your backup may revert hardened security settings back to insecure ones. Imagine you had a setting
crypto_algoritms=A1,A2,A3, then a problem is discovered with A1, and it is removed from the settings. Restoring your backup will make your system vulnerable to a problem which is already fixed for everyone else, so this vulnerability may stick to your system for a long time.
If you want to make such backups in a useful way, you have several options:
keep a full image backup. Requires a lot of space.
patch to backup the changes you have done to
/etc. You may occasionally run into problems, but at least
patch will promptly warn you every time there is a problem. Requires very little space
write a script which makes the required changes, and keep backups of the said script. Requires very little space, and can also handle arbitrary commands like installation of missing packages.