I am not a tax expert, but have had some experience. First, don’t throw proof related to your tax deductions away until at least 7 years past the filing (for this very reason). Second, consider how much they are challenging to determine whether it is worth hiring qualified help.
You say your “return” was only $3,000, but I’m assuming you mean your refund since you wouldn’t file a return with deductions on $3,000 income. The amount of your refund really isn’t relevant to whether they will challenge your deductions.
I assume you will never again use the accountants you mentioned. A good tax accountant’s real value is not in the filing, but in defending their work, albeit at a price. Did they say pound sand or that the amount involved isn’t worth you hiring them? If the former, I might withdraw the “fire them” piece, but I would expect some support from them.
If you can produce legitimate documentation, you can walk out unscathed (other than the stress and the time involved). If you can’t produce it or a legitimate copy of it, you’ll end up paying at least some additional money.
Hopefully, the experts will chime in soon.
Oh, and don’t miss an appointment with them. Trust me on that.