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I have couple of long containers from last season(2 earthboxes and 2, 36" long wooden boxes. I notice the soil in them are kind of dense and soggy due to the left over roots(I planted some peppers in them last year). Is it alright to reuse them or should I empty them and fill em with new potting mixes?

Empty them into a wheelbarrow or something. Mix the old soil with some fresh soil and compost, stir it all together and refill. No point in wasting the old soil, but it does need some refreshment.