There could be a couple of issues here. You are already aware that for some reason the rifle has lost it's pressure.
I'd advise not trying to fill the rifle, any further, unless you can confirm the cylinder valve is working correctly.

Firstly, I'd suggest confirming that your cylinder has enough pressure as your cylinder could be empty. You'll need to get a blanking plug from Best fittings, or borrow one.
Fit the plug in the end of the whip and crack the cylinder valve open.
The bottle gauge will then read the pressure in the cylinder as the pressure in the cylinder and whip will equalise.
You really need to have more pressure in the cylinder, than the rifle fills to, or you only get a part fill.
When you've gone through that, and you are sure you have enough pressure in the cylinder, and the cylinder gauge works, then try a fill on a mate's "known" rifle just to be sure.

If you have confirmed you have enough air, and gauge is working then carry on
When your rifle is connected to your dive cylinder, and you open the cylinder valve, the cylinder valve shows the pressure in the whip. When the fill valve opens on the rifle, the cylinder gauge then shows the equalised pressure in the rifle and whip.
When you decide to close the cylinder valve, the pressure in the whip / rifle, should remain static on the cylinder gauge until you operate the pressure relief valve on the cylinder. At this point, the rifle fill valve will seal, and the whip pressure is vented.
If the cylinder pressure shown on the whip falls, when you close the valve, you have a problem with the cylinder gauge.

I'm (possibly wrongly) assuming that your PH6 bullpup, has no gauge. This makes things a bit harder as you may have a rifle fault, though you may not.
If rifles are shot low in pressure, and you can't judge this if you have no gauge, if there is too little air pressure on the exhaust valve the valve can open and the rifle will empty. This is caused by the hammer spring forcing the hammer onto the exhaust valve preventing it sealing.
This can prevent a rifle filling properly, and its then necessary to cock the rifle, to take the pressure off the hammer, allowing the valve to seal.

So to summarise. Check the cylinder gauge is operating and that you have enough air in the cylinder, before trying to fill the rifle any further.