I think your concern is what "happens" to the transfer fees from an accounting perspective. I think the answer is CoinTracker will assume you are still holding those coins. This isn't a problem because in CoinTracker there will never be a realized gain/loss on those coins...it will basically think you hold them forever. Although, this could possibly become an issue if we ever have to pay taxes on unrealized gains.
For now the only issue I see is differentiating short and long term gains. Suppose in a few years you buy 1 BTC and sell 1 BTC within a month of each other for a gain. Since the 0.0005 transfer fee was "held" for a few years, CoinTracker will treat this sale as 0.0005 long term gains and 0.9995 of short term gains (if using FIFO).
