Here's the way I've done it.
1. Create a brand new Nutcracker sequence with the same music and import the Audacity timings.
2. Add at least one model and one or more effects, and then save it, but
save it with a different name than your "existing XSEQ" file (so it doesn't overwrite it)
3. Exit xLights/Nutrcracker. Open your xLights folder. In it should be your newest XML and XSEQ file plus your old XSEQ file.
4. The XSEQ file that you just created in Step 2 - delete it.
5. Rename (or copy and rename the copy) the new XML file from Step 2 to EXACTLY match the good XSEQ file.
6. Open xLights, go to the Nutcracker tab, and find the XSEQ file. When you open it, it will find the matching XML file with the timings and you will see them in the list.
I've done this several time and it has worked well. Don't skip a step unless you have good backups.