@Digital Shamans -The behaviour you are experiencing does seem to hold true when using both Ctrl+Z or the undo button in the Miro interface, both in the browser and desktop app (at least in Chrome on Windows 64-bit).
I suspect retaining selection information on undo was never considered as the purpose of undo to revert a change and selecting objects does not change their state.
If you were not already familiar with the shortcut, and your nodes are fairly close together, you could use Shift+drag rather than Ctrl/Cmd+click to multi-select the nodes again.
If you would like for Miro consider making this a better user experience, I’d recommend adding “Remember object selections on Undo” as an Idea in the Wish List category.
If you do create a Wish List Idea post, I would also recommend that you post a link to it back here, so that future readers of this post can quickly get to and vote for your Idea.
Lastly, don't forget to vote for your own Idea.