The application I've developed allows users to make calls, but if the contacts are not in the phone's contact list, they can't see the name of the caller when they receive a call.
Using Blocks, what you can do with the Phone Call component is PhoneCall ; what you can do with the Contact List is in ContactPicker.
It appears it is not possible to do what you want to do with the System phone app which App Inventor polls using the ContactPicker and PhoneCall. You cannot completely delete and replace your users system Contact List. An extension might be the solution but the advice provided by @vknow360 is only a partial 'solution' using his extension. So what might be possible to finish your app?
- decide to use Android Studio etc. to create your own way to handle phone calls and contacts to circumvent the system phone call or
- use your own Company allowed contacts list of phones that are valid intercompany calls to achieve as much of what you hope to do using App Inventor as advised by @ChrisWard .
Here are some possible Blocks to consider (not tested) that may help you continue your development using AI2 blocks. Something like this is what is possible as far as I can tell.
The PhoneCall component can identify a phonenumber; the blocks show how to associate that number with a user name. Does this work?
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I thought it is good practice to not give developer complete control over the device.
Once someone erased sd card in his phone using FileTools extension. 
So it would be better to delete only what you have created, though what @rmcpdias is looking for is possible.
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vknow360Regular
If you could create such a function I would be eternally grateful 
Please don't be offended, but since is such a tall order, maybe we could discuss some kind of monetary compensation?
Extension has been updated.
Now you can get rawContactId from phone number.
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You can ask for paid help here:
But please do not request methods to breach Google Android security
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I think the concept of your contact management app is superb. Every company / organization need such central data contact details real time updated and accessible through mobile. I am trying to make same sort of contact management app for my community. I would like to know if your app is lauched on play store and running ?