I'm confused. So is the bottle empty while it's running? But when it cools down coolant does in fact return to the recovery bottle? That's how it's supposed to operate, with the small exception that the recovery bottle shouldn't be completely empty as it runs.
"Level changes are to be expected as coolant volume changes with engine temperature. If the level in the bottle is visible through the site window centered between maximum and minimum mark at normal engine operating temperature, the level should return to within that range after operation and elevated temperatures." Page: 7-6
AND
"Air is removed from the system as it gathers in the coolant deareation pressure bottle and is released into the atmosphere through the pressure valve located in the pressure cap when the pressure reaches 16 to 18 psi. The air is replaced with coolant from the coolant recovery bottle." Page: 7-13
AND
"The engine cooling system will push any remaining air into the coolant bottle within about an hour of normal driving. As a result, a drop in coolant level in the pressure bottle may occur." Page: 7-15
That all would suggest to me there's not enough coolant in the system. Or huge pocket. Or an unidentified leak or vacuum leak in the coolant system.
If you're not seeing any leaks, AND the bottle refuses to hold coolant while operating temps, I don't know what to tell you. What color is your oil? Does it look like coolant is mixing in it?