I should think so, at least in any other such fights in the Legend (such as when fighting a horde of zombies with a few Archmages) the losses remain. But you can try and check - check your "Tactician" medal and the number of no-loss battles before and after the botany battle.
I'm not sure which diploma I'll take this time... last time I used Lizardmen, so it was obvious, but now I am going with a (mostly) human army. What was the third one btw?
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