Unfortunately the current implementation of the editing the route causes rapid creation and execution of new code which any anti virus program will check before execution and this is slowing down the whole sim.
As of now the only workaround is to exempt the x-plane folder from live scans in the settings of your AV program. For Windows Defender you can find instructions on how to set up an exclusion at https://support.microsoft.com/en-us/help/4028485/windows-10-add-an-exclusion-to-windows-defender-antivirus