Further developments on this question:I've found that the ORDER of timing elements and any LINKS (for simultaneous starts) are missing when creating an alternate layout, but the timing DURATIONS are still intact for each element. So, when creating an alternate layout, you have to print out a screen grab for each page's timing panel (so you have a quick reference), re-order the elements to match the original, and re-link any that were linked for simultaneous start. That seems to get things back on track. If you have a lot of alternate layouts, that will be fairly time consuming. But as far as I can tell, there is no way to preserve the order and links in the timing panel when making alternate layouts. At least it seems we don't have to reset all the durations! Please confirm that this is what you are finding as well. Thank you! MC
It doesn't look like the OP followed up by sending us the files related to that question.
There is what may be a related bug in InDesign in which text anchors get broken when a new alternate layout is created. I suspect animation timing could be similar.
I'd be happy to take a look at your files or a sample file that recreates the issue if you can send that to us: