In my farm I have one APP server and 2 WFE servers. Currently the Microsoft SharePoint Foundation Web Application service and Microsoft SharePoint Foundation Workflow Timer service are disabled on my APP server.
I just received an email from a vendor that their new version of the product that we use requires the Web Application service to be running on ALL of the servers including APP servers.
Here is my question: Can it affect/brake Nintex if I enable it and also do I need to enable the Workflow Timer service as well?
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Which version of SharePoint are you using?
As far as I know, this change should not affect Nintex.
I do think it might be a good idea to enable the workflow timer services on the APP server as well, to keep things consistent (https://support.microsoft.com/en-us/kb/2674684), although, I do not see it being mandatory as your users are not hitting the APP server directly.
The bigger issue you might have is with Licensing, as Nintex is licensed per Server where Web app service is enabled. You might want to check up on that.