When you upgrade the garden, you should be notified that your plants will die in the upgrade. I know it doesn't make a lot of real world sense because it's not even touching the plants, but I didn't bother to spend the extra time to make content for an accessible garden plus an under construction greenhouse.
If you played Beta 3 of v0.18, that in-development build was buggy and cause this permanent bug to be present. You may need to restart your save.