Tree seedlings come up in my flower beds every year. For the past few years, I have transplanted them around the land. I do have one small tree that grew from a transplant maybe 10 years ago.
Yesterday, we dug up 4 baby cedars, and brought netted tree tubes to protect them from deer and other animals the first years of life. We also found a number of other transplants from previous years, Douglas firs and cedars. Just one dead tree was found.
The daffodil bulbs fare just fine even when something is dug up around them. I have separated daffodil bulbs in the early spring, but don’t suggest it as a rule.