I'm afraid the news is not good. If you use weedkiller, you will also damage the surrounding perennials. I realise that this is a lot of work, but to really control the wild onions, you would be wise to dig up your perennials and clean the bed of wild onions. Even the tiniest bulblet starts over as I'm sure you've discovered. When you have dug deep and cleaned the bed of onions, you can replant the perennials. If you want to use weedkiller (such as RoundUp) apply it at this point. As you replant, be sure that there are no onion bulblets hiding among the perennial roots. Another approach is to put down a layer of landscape cloth in the winter and cover it with mulch. Cut out holes for the perennials to grow through and be careful not to smother them with mulch. The onions should come under control after a couple of seasons.
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