You can remove a site from a SharePoint Online app.
Procedure
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From the navigation pane, go to Protect > Office 365.
The Office 365 Overview page appears.
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On the Apps tab, click the app.
The Overview page of the app appears.
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Perform one of the following tasks depending on the entity you want to remove:
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On the Sites tab, in the row for the site that you want to remove, click the action button
, and then click Manage > Remove from content. -
On the Content tab, in the row for the group that you want to remove, click the action button
, and then click Manage > Remove from content.
A confirmation dialog box appears.
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Click Yes.