Learn Russian: Там было наводнение, это форс-мажор, так что мы делаем возврат. - There was a flood, this is force majeure, so we are making a refund.

Here, так что functions as a single conjunction meaning so or with the result that, and the comma must come right before the entire phrase. If you put the comma between the words (...так, что...), it changes the grammar and means in such a way that.

Is делать возврат the standard way to say issue a refund?

Yes! In retail and customer service, делать возврат (literally to make a return) is the most common way to say give a refund or process a return. You might also hear оформить возврат (to process/register a return).

Why use Там было instead of just starting with Было наводнение?

Starting with Было наводнение perfectly translates There was a flood. Adding Там (There / Over there) in this business context usually implies in that specific location or in your area, distancing the company from the event causing the delay.

форс-мажор is clearly a borrowed compound word. Do I need to decline both halves of it?

No, only the second half declines. It functions grammatically as a single masculine noun ending in a consonant, so if you needed to use it in the prepositional case, for example, it would become при форс-мажоре (in case of force majeure).