I think I found another glitch...

[xSuperMario64x]

This has to do with the fruit counter that shows how many trees you can dig up, how many rocks you can break, etc.
For some reason if you eat a fruit/bamboo shoot/egg to increase your energy counter, and then you enter/leave the player's house, the counter is reset to zero. I've demonstrated this glitch in the video below:

https://twitter.com/x/status/1256785037061545984

Notice that when I'm inside the house, the counter is set to 1. But once I go outside, it's set to 0 again.
I initially figured out the glitch when I was in terraforming mode, but it works even in normal gameplay. I haven't tried it with any other buildings, just the player's house.

This was really frustrating for me to figure out initially, since I've been doing a ton of landscaping recently. I did this and then tried to go out and move a cedar tree that was in the way, and I was disappointed to find out that I consumed 4-5 of my wood eggs just for them to disappear when I left the house. What a waste of resources.

 

[FraudulentDimetrodon]

My egg fruit counter is working as normal, both in and out of terraforming mode. I also used my house to test. So I think something is different with what you're doing.

This is a really silly question, but have you tried just restarting your game? There was a recent glitch involving the May Day tour where your held item doesn't persist upon going in and out of buildings after going on the tour. It was fixed upon a simple restart. Maybe this is a similar thing?