Now my company wants to update app with significant changes. In new app version will change absolutely whole design and internal logic (code).
Will the market allow such an application to be released? Wouldn't that be an intellectual property infringement? I would like to see official links with information about it.
Updating an app and completely replacing everything about it is fine. Sometimes you rewrite apps, that's ok. The only requirement is that the signing key remain the same, and the version code increase.
As for UP infringement- if your company owned the original app, how would that even remotely be IP infringement? You own the rights to the IP, that includes the right to no longer offer it for download, or for you to reuse the name for a new app.