How can I resolve random SKU updating issues with product variants?

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SO not sure whats happening but I will give you a description the best I can. We have 32000 items so we did a bulk upload, once we seen how it looked with boots and clothing we decided to make variants for sizes and what not. At first our app we had made by a developer was updating the original sku and the copy in the variants. Now its sort of doing them but it's random, some are working where others are not. Shopify support said its because of duplicate SKU's but some work, they said it's our developers issue. The developer cannot replicate the issue, again I added some new products and set the SKU's this time direct as variants and they update fine, well not really I added the first option as a sku and then added the variants and the original sku has vanished. I did add it back as a variants but it will not update inventory. I also deleted any duplicates on a set of boots to see what happens and they have not updated inventory via our app. In my logs there are no errors says SKU number updated by X amount and completed. Should I remove all of the variants and re add everything, it's going to be a PITA but if its will fix it it maybe worth the time. None of whats happening make any sense, it's just very random.

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