So the mixer doesn't protect against this scenario...
Because it is not a scenario that needs protecting against. It is extremely unlikely to occur and if it did it would not decrease your privacy in any way.
How would re-using funds that were supposed to be mixed not decrease privacy? That's like using funds that were never mixed.
These funds would be just like i never used mixer. I know that you wont receive all chips from single address, but even getting a part of it - it's making you receive part of your input "dirty" funds.
And you dont want to use them, do you? You want to get rid of them. And there's chance you can receive these funds in chipmixer.... by using the service often, not one time per month.
Same as if i have funds and i split them now to chip values? Is it mixed? Is it secure? No
Let me give example.
01.01.2019 - you try to mix coins with chipmixer, you receive your keys..
04.01.2019 - chipmixer splits coins into chips, this happens with funds received on 01.01.2019.
12.01.2019 - you try to mix coins again with chipmixer, by such coincidence you receive chips that were partially created from funds that you sent on 01.01.2019 and that were converted to chips on 04.01.2019
This means that part of your money was not mixed and you're most likely not even aware at all and can be making critical mistake.