When you say soil do you mean soil-less potting mix? Were they covered while sitting or exposed to rain? There is some discussion in the Tips and Tricks section under the Topic: soil wicking question for second year EB's thread.
If they were covered, it would be a case of scooping out the fert strip and top inch of old mix, removing large stalks if present and rejuvenating the box per EB instrustions. If left uncovered the old fert strip and leftover salts were washed down into the mix and complicated things.
Yes, I forgot its potting mix not soil. It was covered and I removed the top layer with fert strip. We just didn't bring it indoors afterwards. I had such beautiful delicious tomatoes last year I did want to make any mistakes.