We recently accepted a $1000 membership dues payment (our first), then found out that our Form 1023 did not go through so, technically we are not yet a tax-exempt organization (although we did apply for the EIN as a nonprofit). At this point in the year, I doubt we will get tax-exempt status before December 31. Should we/must we return the dues (from an international organization) or file a regular tax return and just pay the tax (if any, since we don't have any other income yet)?
It isn’t particularly unusual for the IRS to ask questions about a pending Form 1023 application for recognition of charitable exemption. Most organizations are able to provide enough information to qualify for (c)(3) exemption.
In the meantime, assuming you still have a good faith belief that you will qualify, I wouldn’t return the money. As an international organization, the donor may not even need a charitable contribution deduction and may just want to support your work. You can ask that question if you are permanently denied charitable status.
Assuming that you are a calendar year tax filer, you don’t have to file any sort of tax return until May 15 and can get an extension even for that until November 15. And if you don’t get any more money, you can file the Form 990-N electronic postcard just to let the IRS know you exist and claim (c)(3) status. In other words, you have plenty of time to get this straightened out before you have to do anything.