No person, including Youth, may
submit more than one valid application per genus for the First Come
process, with the exception of javelina (see the javelina bag limit description).
A listing of leftover permits is available online at www.
azgfd.gov under “Big Game Draw” or at any Department office. To
submit first come applications by U.S. mail only, please send to: 5000
W. Carefree Highway, Phoenix, AZ 85086, ATTN: DRAW/FIRST COME.
According to above from the 2015-16 regs, I do not think you will lose your bonus points, so long it is not for the same unit/hunt code. In my mind, what make this confusing is Arizona's choice of language.
In AZ, you don't get preference points in the classical sense (e.g. Colorado). What you get instead is a bonus point which I believe is akin to buying an extra raffle ticket to increase your odds of winning a prize (or a hunting permit in our case).
Since in AZ, you can purchase a bonus point (no refund), it is YOURS and your ability to keep those bonus points should be independent of your other applications. In other words, you should still be able to purchase and bank your bonus points and still draw a left over permit so long as your bonus points are under a different hunt code that what you wish to draw a leftover (first come) tag for.
For example, I purchased a bonus point for an archery spring javelina hunt in unit 21 last year. I have banked one bonus point for that unit and now lets say I want to apply for a leftover archery javelina tag in unit 22 and get it. It is hard for me to imagine AZGF taking away the bonus point i purchased for unit 21. They would essentially be doubling their money because you still have to pay for your leftover tag and you would have to purchase new bonus points. If that is the case, its a scam and should be changed.
This is my understanding but I could be wrong. A call to AZ fish & game should settle it and if you find out for sure, please share as I think you have happened upon a really good question here.
Whatever you decide, know that only one deer is allowed per year so if you tag out during the fall rifle season, your OTC archery tag is not longer valid for the December OTC archery hunt. Likewise, if you were to come and out and tag a deer during the August OTC archery season, your gun tag for fall is no longer valid.
This would all be so much easier if AZ just sold leftover tags OTC like other states.