Protecting PHP web application

I have a VB6 application (LIS - Lab Information System) which I am in the process (actually 80% complete) of converting to web app using PHP & MySQL.

I already have so many clients/Labs (most of them have many branches) who use the desktop version and willing to use the web version!

My strategy is :
1- Using XAMPP locally for each branch for the sake of performance and unavailability of internet connection for any reason (and believe me it happens a lot here in my country).
2- Have a service which uploads new added/updated records of each branch to the online server every few (customizable) hours.
3- Users including the lab employees, patients or even physicians can log in to retrieve data/results, stats or reports according to their privileges from the client's website.

With my desktop app I was able to protect my app (well, to some extent as there is no absolute protection), how can I accomplish this with PHP?!

Uploading the web app to my own server and giving access to registered clients only is not an option for many reasons including the problem with internet connection I mentioned earlier and more importantly most of my clients need to have their patients data to be under their own control and on their own servers!

Any suggestions is mush appreciated and thanks in advance.

Hey labmany, haven't used any but know there's a few php "compilers" floating around, can't vouch for any of them working with PHP7 however.

I would tend to drop in a phone home function that checks an embedded serial number against a database for example.

What is it you're trying to protect? the code or the data?

-tg