Why
If you deploy your app with an deployment server, the deployment server replaces the whole app / ta folder to all heavy forwarder / search indexes / etc.. This replaces also the local folder in which the seq.json file is in place.
What
Remove the usage of external file for a sequence number and use the checkpoint function from the splunk python helper scripts.
https://docs.splunk.com/Documentation/AddonBuilder/2.2.0/UserGuide/PythonHelperFunctions
How