Issues with changing sqlite database method names and strings

What I am doing:

I am creating an app. Some of the names of the items in my sqlitedatabase are being and some are being removed. I am using android studio and "Refactor" to make these changes. Everytime I make these changes though, I start getting issues within my manifest. What I am saying is let's say I have items A, B, C, D, E and don't want D and E. Also I want to rename A, B and C to X, Y, Z. Also I want to rename some of the methods in the DataBaseManager file, like updating items in the DB, changing items, etc. So if the method is called updateX, I want to rename it to updateZ.

Question: How do I remove elements of my database without these errors? Below are the errors I am getting:

Gradle gives me errors such as :

Missing "name" key attribute on element activity at AndroidManifest.xml:22:9
Execution failed for task ":app:processDebugManifest"

Also, it points parts of my manifest like these:

    android:label="@string/app_name"
    android:theme="@style/AppTheme"

and tells me the references are not there. However, they are there in my strings and styles xmls.

The other problem is the app pretends my main activity no longer exists.