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Yes that's how the multimixer works. It keeps all of the effects in the "base" ingredient and adds any from the other that it can ie. where there are empty slots.
If the ingredient is "full" ie has 4 effects. Then you will need to remove an effect before you can add something to it. However, it sounds like you have been quite unlucky and you have a lot of "non-removable" effects. If this is the case, it might not be possible to combine them without the Centrifuge. The centrifuge is a late-game machine which *swaps* effects, so you don't need to remove things first.
It's one of the tricky bits of the game, and what makes it a bit of a puzzler at times!
Also you need to consider "Is it worth it for me to even do this?". Sometimes it's so expensive to remove an effect and add back in another that you're better off just making something else.
Hope that helps,
Tim
http://bigpharma.gamepedia.com/Multimixer
It's also worth noting that those "cannot remove" side effects can, in fact, be removed! If you have the Marketing & Malpractice DLC, there's a machine added called the Booster Mixer. Basically, it'll take a booster (yellow effect) from one ingredient and replace whatever is in that slot in the main drug. It's the perfect way to edit out those troublesome cannot removes.
Alternatively, you can use centrifuges and/or multimixers to shift those cannot removes into a drug which you just throw away (using the analyzer as a trash can), but that's a lot pricier and more complex.
Don't worry about throwing out a "trashcan" product - sometimes you just need to shift bad effects out and there's no use for where they go. (Big Pharma isn't a totally clean industry!) But the Booster Mixer really helps cut down on the number of times you need to do that. Even if you're adding boosters that won't do the drug any good, it's still better than a non-removable side effect that could kill patients. (And reduce your sales.)
I hadn't thought of it that way. Nice tip!