I am able to reproduce this issue in the Blockly playground, and in fact it is even stranger than you describe: when I open the mutator flyout any blocks attached to the elseif or else inputs (but not the if inputs) are moved the far side of the workspace—but they seem to remain attached, and if I drag the block (even with the mutator still open) they will snap back to their correct location.
This seems to be a bug in Blockly, and I have accordingly filed
issue #6953 to track its resolution. Follow that issue for updates.
Thanks for reporting this!
Christopher