Repro steps:
  1. Prepare three nodes. (I'll call these X, Y, Z.)
  2. Connect flow control X to Y. (I'll call it line1)
  3. Connect X to Z. (I'll call it line2)
  4. Delete the line1
  5. Reload graph. Then line2 disappears.
Environment: VRCSDK3+UDON-2020.04.03.13.19
If you reload after step 3, the line1 is already deleted. So I guess the line1 is already deleted internally on step 3. Step 4 deletes "phantom" line. Also step 4 deletes line2 as a side effect of incorrect operation.
Workaround: Reload graph manually after connecting new line. Or delete old line before adding new one.