fix_tree.py: ValueError: list.remove(x): x not in list

[joverlee521]

Error was originally reported on 25 July 2024 via Slack, with #264 was an attempt to work around the bug.

The automated hmpxv1-big build also ran into the error on 14 December 2024:

[batch] [2024-12-14T18:36:07+00:00] Traceback (most recent call last):
[batch] [2024-12-14T18:36:07+00:00]   File "/nextstrain/build/phylogenetic/scripts/fix_tree.py", line 63, in <module>
[batch] [2024-12-14T18:36:07+00:00]        	  reconstructions: 8981
[batch] [2024-12-14T18:36:07+00:00]     reversion["child"].clades.remove(reversion["grandchild"])
[batch] [2024-12-14T18:36:07+00:00] ValueError: list.remove(x): x not in list

Seems like a stochastic error since the re-run of the hmpxv1-big build has successfully finished the fix_tree step.