Instead update the web.config file to include the applicationInitialization configuration element. Specify custom initialization actions to run the scripts.
Note: Some apps might require custom warm-up actions before the swap. The applicationInitialization configuration element in web.config lets you specify custom initialization actions. The swap operation waits for this custom warm-up to finish before swapping with the target slot. Here's a sample web.config fragment.
<system.webServer>
<applicationInitialization>
<add initializationPage="/" hostName="[app hostname]" />
<add initializationPage="/Home/About" hostName="[app hostname]" />
</applicationInitialization>
</system.webServer>
Reference:
https://docs.microsoft.com/en-us/azure/app-service/deploy-staging-slots#troubleshoot-swaps