How to Restore Phone App in CM13?

It must be a problem with the ROM if it is not showing the app disabled through Settings app like this:

_{(Click image to enlarge)}

Anyhow, if the Settings app doesn't show it then I see no way to solve this problem without root. If the following steps do not work then your ROM is faulty because they worked for CM13-snapshot in my Nexus 6. In case you do not know, root access can be enabled in CM13 from Developer options.

A disabled app is a user specific restriction and the restriction ends up in the file /data/system/users/USER_ID/package-restrictions.xml. USER_ID for primary user (owner) is always 0.

Find the entry responsible for disabling your app using the app's package name and either remove the whole line or make tweaks there. I'm instructing with a tweak. Here's how the restriction originally looked like:

For the case in question: In the line depicting the cursor and containing the string com.android.dialer, integer to enabled represents the state of the package and enabledCaller is the caller which instructed the package to be disabled. You can either remove the whole line or change enabled=3 to enabled="1". (Source)

Do a full or soft reboot and you would find your app enabled.

The alternative method is to use a terminal emulator app or adb with adb shell command to execute these:

su

pm enable PACKAGE
# PACKAGE refers to package name of the app to be enabled

If you don't know the package name of your app, follow View app's full package name?

Another alternative: While I didn't try, I've full faith that Titanium Backup
would offer the option to unfreeze your app. There may be other similar apps that can help you out.

If the said solutions make no effect on the app's status, ditch the ROM.