I didn't see this when you first asked about cleaning. I would say it is definitely a good thing that you did clean it now so you could remove the two that had died and the last of the eggs. It sounds like even though you "distrubed them LOL" that they are happy to have a nice clean home. In semi-tame to tame birds it is usually fine to clean out the nest box when it gets too dirty or smelly just being careful of eggs (usually don't clean until all hatched etc). In scared or untamed birds it can cause them to peck at their babies and step on them etc possibly injuring them if you disturb them too much in cleaning. Either way if it is getting too smelly etc it does need to be cleaned just be careful how much disruption you cause and make sure mom and dad don't get too aggressive with babies. In your case even though they were upset it seems they were just fine to have fresh bedding etc.

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