Can't change tel protocol handler in Windows 10

You can save this (you should change dialer %1 to your own command line):

Windows Registry Editor Version 5.00

[HKEY_CURRENT_USER\SOFTWARE\Classes\callto]
@="URL:callto"
"URL Protocol"=""

[HKEY_CURRENT_USER\SOFTWARE\Classes\tel]
@="URL:tel"
"URL Protocol"=""

[HKEY_CURRENT_USER\SOFTWARE\Classes\dialer.callto]

[HKEY_CURRENT_USER\SOFTWARE\Classes\dialer.callto\Shell]

[HKEY_CURRENT_USER\SOFTWARE\Classes\dialer.callto\Shell\Open]

[HKEY_CURRENT_USER\SOFTWARE\Classes\dialer.callto\Shell\Open\Command]
@="dialer %1"

[HKEY_CURRENT_USER\SOFTWARE\Dialer]

[HKEY_CURRENT_USER\SOFTWARE\Dialer\Capabilities]
"ApplicationDescription"="Dialer"
"ApplicationName"="Dialer"

[HKEY_CURRENT_USER\SOFTWARE\Dialer\Capabilities\URLAssociations]
"callto"="dialer.callto"
"tel"="dialer.callto"

[HKEY_CURRENT_USER\SOFTWARE\RegisteredApplications]
"Dialer"="Software\\Dialer\\Capabilities"

as .reg file and import it in the registry. That should add dialer in the list of programs you can choice for callto: and tel: protocols.

This Microsoft article may answer the problem :
Lync 2013, Lync 2010, or Office Communicator 2007 R2 becomes the default application for protocols after user signs in.

Summary

When you sign in to Microsoft Lync 2013, Microsoft Lync 2010, or Microsoft Office Communicator 2007 R2, registry settings for the following protocols are overwritten:

• TEL
• CALLTO
• SIP
• SIPS
• IM
• CONF

When this occurs, the application that you signed in to becomes the default application that supports these protocols.

Workaround

1. Open Registry Editor. To do this, follow these steps:

   • In Windows 8.0 or Windows 8.1, press the Windows Function key to open the Start screen. If you are running Windows 7, click Start.
   • Search for regedit.exe by using the Windows Search feature.
   • Right-click regedit.exe, and then click Run as administrator.

2. If you have installed Lync 2010 or Office Communicator 2007 R2, locate and then right-click the following registry subkey: HKEY_CURRENT_USER\Software\Microsoft\Communicator
   If you have installed Lync 2013, locate and then right-click the following registry subkey: HKEY_CURRENT_USER\Software\Microsoft\Office\15.0\Lync

3. Point to New, and then click DWORD (32-bit) Value.

4. Type DisabledProtocolHandlerRegistrations as the name of the new registry entry, and then press Enter.

5. Input the correct information about the third-party application that you want in the registry. For example, to change the default application that supports SIP from Office Communicator 2007 R2 to a third-party application that you want, follow these steps:

   • Locate and then click the following registry subkey:
     HKEY_CURRENT_USER\Software\Classes\sip\shell\open\command
   • Double-click the default registry entry. Then, change the value to reflect the application that you want to use instead of the Microsoft UC clients.
     Note: The default value in the registry entry points to the Microsoft UC client.

   • Prevent Microsoft UC client information from being rewritten to the registry setting that you changed in step B. To do this, add one of the following values to the DisabledProtocolHandlerRegistrations registry entry:

     TEL: 0x0001
     CALLTO: 0x0002
     SIP: 0x0004
     SIPS: 0x0008
     IM: 0x0010
     CONF: 0x0020
     

Notes

• You can sum the values in the list if you want to prevent a Microsoft UC client from being the default application for multiple protocols. For example, to prevent the Microsoft UC client from being the default application for SIP, enter 0x0004. To prevent the Microsoft UC client from being the default application for CALLTO, enter 0x0002. To prevent the Microsoft UC client from being the default application for both SIP and CALLTO, enter 0x0006. To prevent the Microsoft UC client from being the default application for all the protocols, enter 3f.
• The values in the DisabledProtocolHandlerRegistrations registry entry will be unavailable if you change them when you sign in to the Microsoft UC client.