TLDR: Yes, you will lose chutes from version 1.0.1
Kerbal Space Program has an advanced physics engine and while the planets of the Kerbol system are different to the Sol system, the mechanics are similar:
In real life a re-entering spacecraft is hitting air at huge speeds and that is heating the vessel. The chutes undergo huge stresses when deployed - both from aerodynamic pressure and heating. If these stresses are too great, the parachutes could simply tear off.
Version 1.0.1 of KSP brings this real life danger into the Kerbal universe. Now, if you're moving too fast when the chutes deploy, they can be "burned up". Or, even if you're not undergoing heating, the chutes can be destroyed due to aerodynamic pressures.
How can I avoid chute loss?
Not losing parachutes from heating is easy: Don't deploy them when your vessel is burning up. You can tell if the vessel is burning up by looking at it - is it on fire? Don't deploy chutes.
Not losing parachutes from aerodynamic stresses is also easy: Don't deploy (even partially) when you're going fast. How fast is "fast"? I've conducted some tests and it looks like 1000m/s is the magic number. Although it may change depending on atmospheric conditions.
Edit: After version 1.1 chutes can be destroyed going slower than 1000m/s. Look at the chute icon in the staging, it changes colour based on whether it's safe to deploy or not.
There are a number of issues with VTOL. Biggest one is that the vectoring on engines becomes less and less efficient as the center of thrust is moved higher up towards center of gravity. If center of thrusts ends up above, you actually get engines actively trying to flip the craft over. So first thing is that if there is room at all, move the lifter jets down.
Second issue is that gimballing initiates when you fire a stage. If you just activate the engines via action groups, you get no gimball control. So fire all of your engines in one stage, then shut down these you don't need with action groups. When you re-activate these with action groups, they'll work as supposed to.
Finally, as fuel is used up, center of mass shifts. Your VTOL might start out perfectly balanced and hover steady, and then a few seconds later start turning over. Before you can properly react, the thing is flipping over. You have to make sure that fuel is being used up symmetrically around center of mass. Not an easy task, but that's the only way you'll get a good VTOL.
Best Answer
Does the Ferram status window start saying "Minor Stalling Detected" at any point? I suspect that your wings are losing lift due to stalling, and if your wings are stalling, then your control surfaces are also likely stalling, which means they can't bite the wind to bring the plane back under control. Without video to see exactly what you're doing wrong, or how the plane is behaving, that's about all I can tell you.
With Ferram, you have to start out simple, and increment your designs. It's unforgiving in its realism, just like real aeronautical engineering. If you're having a lot of trouble with this type of thing, take a look at Scott Manley's videos on aircraft design (part 1, part 2, part 3). He shows how to improve inherent stability, among other things.