I have done bond for deeds, both as a broker, and a principal - so allow me answer your question with confidence - You will both keep, and lose the benefit of your deposit. You keep it in the sense that the deposit is applied to the original purchase price and reduces your principal that will need to be financed, eventually, to the owner of the bond. (The seller who still holds the deed). However you will - probably- lose the cash benefit as applied to down payment in the eyes of the traditional lender when you go to refinance it.
Generally, traditional, Fannie Mae/Freddie Mac/VA/FHA lenders will not look at it as a "refinance" - with you holding equity - but rather, they will have you draw up a new purchase contract for the amount that is remaining with the original seller.
That may mean that you, while making bond for deed payments, must also save additional money for the required down payment when you go to get permanent financing. That can be problematic, and you should know this going in. One answer is to plan to get 100% financing, or a low - say, 3-5% conventional loan... but you're going to have to "suck it up", and overlook the fact that you're paying mortgage insurance - and more down payment than you originally paid the seller - even though you may, very well, by this time, have significant equity, depending on your situation. That's a tough one to swallow - and seems terribly unfair - but, alas - "life is not fair" and you aren't going to change conventional loan guidelines because they don't make sense in your situation..."it is what it is".
Sometimes, the plan to permanent conventional financing is a two step one. One may wish to first, do a low down payment conventional, or traditional loan - say at 100%, 3 - 5% down financing, with PMI - or taking a slightly higher interest rate which includes the PMI as the initial loan to convert the Bond for Deed contract to a traditional sale. Then step two, you plan to refinance after 6 months. At that point, the lender WILL consider it a refinance, a new appraisal will be done, and your equity position will be properly recognized and reflected in the loan. It may even be possible to do a cash out refinance and recoup any excess down payment you have made, if you wish, provided that you do, actually have the equity at that point. In all fairness, I would ask that you do not contemplate refinancing prior to 6 months. People don't usually know this, but your mortgage broker can actually be charged back and penalized by the lender if you instantly refinance your mortgage, before the 6 month point. That's bad Karma - and it isn't kind to do to someone. I truly believe that we must, in business dealings, as well as life, treat others as we would hope to be treated.
Going with that plan - you run the risk of interest rates climbing during that 6 months, and ending up with a more expensive loan than you had hoped for. There is no such thing as real estate investment without some degree and manner of risk. But there also is no reward - in real estate - or anything in life for that matter - without some degree of risk. The key is to maintain a balance that works, personally, for you.
Do not listen to the naysayers who warn you NOT to do a Bond for Deed - ever - It is a useful, and valuable tool - especially in some situations where permanent financing is not available for you yet - but, due to your circumstances, is extremely likely, and predictible to be available to you in the near future. But, please, DO listen to this advice Don't go into a Bond for Deed with wishful eyes, a hope and a prayer - and unrealistic expectations. It can spell disaster for you if you are not aware of the in's and out's, risks and benefits, and are fully prepared to meet all of them - As with ALL real estate investments.
If you are not working with agents/lenders and other advisors who are fully familiar with what you are trying to do - Please, do yourself a favor, and find advisors who are. They do exist - and a good fit is necessary.
Best of luck to you!