Deploying single project within different Azure App Services can be a common task – one service for test, one service for prelife and another one for production. There is no problem with such scenario. But when you are using Webjobs project, it can cause an issue.
Webjobs are using Storage for various purposes. You must specify AzureWebJobsDashboard and AzureWebJobsStorage connection strings in Webjob configuration.
If you are deploying same project with Webjobs within a different App Service, you MUST SET CONNECTION STRINGS TO DIFFERENT STORAGE ACCOUNT. Otherwise these Webjobs will collide – they will access same metadata because of the same path name. E.g., in case of time-triggered WebJob it can happen that only the first WebJob will be executed periodically and the seconds one never.
Note: There is opened GitHub issue that is still open because of low priority.