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"when you look at the budget vs actual, it doesn’t take into account the amount’s transferred from operating to reserve and gives an inaccurate bottom line."
Are you saying that your P&L doesn't show the reserve expense? Reserves are income when collected and an expense when moved to equity on the balance sheet. I've been treasurer of a couple of HOAs and QB works just fine IMO. The proper way to account for reserves is to record them as income when received and then create a journal entry that debits your Replacement Reserve expense account and credits your Replacement Reserve equity account. That creates the offsetting expense entry on your P&L with a corresponding amount to equity on the balance sheet so those funds can be spent from there when needed.