Yes, you absolutely can brick modules in ways that are not possible to recover, requiring installation of a new part instead. I don't want to mince words here, we are dealing with parts of the vehicle Ford never intended to be modified in the way we are modifying them. It is possible to permanently damage modules and your car. The safeties are off. It is dangerous to your wallet to do this. I had to buy three Parking Aid Modules because I screwed up one, got the wrong part for the second one, and the third finally worked to add automatic parallel park assist. The original one off my car and the other two are sitting in a box in the back of my garage reminding me to read part numbers correctly the first time before searching on fleabay.
There are generally two types of 'programming' you can do with Forscan: AsBuilt config changes and module firmware updates.
Modifying "AsBuilt" configuration flags is _usually_ safe. Save a backup of the original, make sure it's easy to find, then follow guide on the settings you can flip. I've written about those config settings here: https://github.com/Cellivar/ford-c-max/tree/main/systems/modules I've got links to sources where I get my information on those pages, and some of those have been myself , CR08, bookemdano, and others changing flags and seeing what happened.
I say _usually_ safe here because some of those AsBuilt settings are actually one-time-change permanent flags. If you change some of them you can't put them back. If this happens to your Body Control Module or Powertrain Control Module those are expensive and complex to replace. And again, since Ford never intended anyone outside of Ford to touch these, those settings that can't be changed back are completely undocumented and have to be discovered by trial and error. The F150 folks doing this sort of thing have found a number of them in their Transmission Control Modules and, well, that's pretty annoying and expensive to replace.
Module reprogramming is an entirely different beast. Ford provides very little external information about the different versions of firmware for modules, this is again pieced together through trial and error. We know things like "don't update the firmware of the IPC while it's in the car" because people have bricked their IPCs doing this. We know "don't update the BECM firmware on its own" because it turns out the BECM, DCDC module, and a few other things all need to be on a compatible-with-each-other firmware version. Which version is that for each module? That's right, trial and error. "Your car doesn't run until you try every combination" sorts of trial and error. And firmware module updates can take hours.
All this to say:
Nothing we're doing is 'safe to do', it's about making it 'safe-er to do'.
Learn as much as you can ahead of time BEFORE you start messing around. There's a reason I started writing things down into my GitHub space.
Have a backup plan in case everything goes horribly wrong. Backup config files. Backup module firmware versions. Backup your odometer reading. Backup everything so you can put it back in a hurry if you need to.
If you can't live without your car working for a while wait for a better time to mess with things.
Read all instructions and guides carefully before you do anything in them, making sure you understand them before you try them.
Don't expect your dealer to bail you out, they don't know what we're doing and they often know less than you do.
So long as you keep your head on straight, understand what you're doing before you do it, and have a backup plan in case what you're trying to do doesn't work, you will usually be okay.
Usually. Good luck.