It is possible for a skilled programmer to make the ecu do anything.
This includes hiding maps in areas not read by OBD, making duplicates in free memory to create decoys, blocking reading by obd completely, and putting physical protection on the chip to prevent serial reading etc. Depending on the methods used you can work around it, sometimes its easier to just program an original (which is basically what the original map developer would prefer you to do - remember this isn't about locking you in to their tunes, it's just protecting the integrity of their work).
I don't know if the 'professional remap' you are working with employs such tactics, but it is certainly possible. Companies like Revo etc employ it as pretty much the norm, and if you do a search you will easily find people who have been caught out by it.
Unfortunately, thanks to people who rip off peoples files, it has become necessary to do this. I've no sympathy with the pirates as people have tried the same with me.
Is the anti-piracy measure just a lie? :?
It's a toughie because I've found a lot of professional tuners to be generally untrustworthy (thats why I don't mix with many) and so even i take what people say with a pinch of salt, but what I've said above is actually possible if the tuner is skilled enough.
It's annoying because if you try to be a genuine tuner offering a decent service you get it from both sides. Other tuners hate you for being in the business and end users trying to steal your files. The crush between the two does my head in. If only people had morals and ethics...