The fact that a DVD is pulled from the shelves has nothing to do with the fact that another version of the product is coming. It has to do with contracts, legal agreements, terms of usage/sales, ect. The fact that the TimeLife DVDs were pulled is not in anyway related to the fact that Disney is going to release the same content in another form.
When one company (like TimeLife) looses the rights to a property (like The Muppet Sho) and a new company gets them (like Disney) the reason the products may get called back is because of the terms of the original agreement with the first company (in this case TimeLife). It's not because it's the "all mighty disney"; if TimeLife's contract expired, the DVD would have been called back even if Henson still owned the Muppets. Even if Disney has no plans to ever release the Muppet Show on DVD ever, the DVDs would have still been called back. It is a legal thing, not a marketing thing.
Although usally when a product get's called back like this there is a re-release later on; the two are not connected.