Did you write your own apps  in full or did you get some open-source source codes somewhere?  Is it possible that some of the codes get hacked by a third party and the generated apk is really problematic?  How many other apps did you encounter similar "problem"?

If the apk is clean and Google Play Protect reports a false positive,  you should ask Google for support.   Their tool does not seem to include any provision to input exceptions.  So, your only option may only be turning it off.

MobiControl has already included Webroot/Bitdefender  to protect Android devices against malware/virus.  Enabling Google Play Protect is basically not necessary.  Besides, if you search on the web on some benchmark reports related to detection performance,  Google Play Protect seems to be much below par.   Finally, I am worried if Google will use this tool, just like many of their so-called free services,  to get user's data (e.g. apps analytics or statistics in this case) for their big data,  hence compromising privacy of individuals or of corporate app/IT policies.

If Google Play Protect is actually blocking a private business application from being installed then my fears around its potential effects on mission critical / line of business deployments is coming true. When I first heard of Google Play Protect and the features of automatically quarantining applications that leveraged old or outdated libraries with vulnerabilities my mind immediately jumped to business applications, like those used in warehousing environments and field services, that often don't actively updated or maintained after deployment in order to preserve stability. What is the point of Google quarantining an app that may have a vulnerability multiple years after it was initially deployed if the device and application are operated within a secured, fire-walled environment? I understand this is kind of becoming an old-school mentality as business environments become increasingly cloud enabled but it could be extremely detrimental for Play Protect to automatically disable or uninstall a LoB application without warning. They should introduce the capability of whitelisting certain applications from the scans or else we may be forced to disable the service entirely in most cases.

I agree with both points. My app in question is pretty simple, but does make use of Zebra Link-Os for printing, along with Realm for a data store. The strange thing is the first time I deployed it worked but the update didn't. Fixing the issue was difficult. I had to get users to manually toggle off Play Protect, then uninstall the app, revoke the profile and redeploy the profile. It was a real pain considering my customers are in a different country.

I've been building mobile field worker type apps way back since 2003, and I even have an app out with 120 drivers running Windows Mobile that this app is replacing. 

If the phone is been enrolled in a work environment, with lock down provisions, etc. there should be a way to trust the app.

I have a similar issue. I can install the app from Google Play but not from a package. In this case we need to install from a package to android classic devices.

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