When installing a package with overwrite option, some items are being automatically deleted where the package is installed.
Will installing a package with overwrite option delete content items?
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If you use
override option while installing a package, it replaces every item and its descendants with items from the package.
So if you have item
A in your application and it has 2 children
A2, and your package contains item with same ID as item
A, after your package is installed, you will have only what is in your package and old items
A2 will be removed.
If you want Sitecore to leave old items, try using
You can read more e.g. here: SITECORE PACKAGE INSTALLATION OPTIONS EXPLAINED