JM Rotted Trunk Hole Holding Water

Bonsai Cowboy

Seedling
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TL;DR - my tree rotted in the middle, so I carved out the spongy-rotted wood and that created a water-holding hole in the trunk. I'm not sure what to do to fix the water-holding hole or to help this tree heal-up. Pics inserted below.

I have had this Japanese Maple (Osakazuki) since 2014 (I think), living in a big garden pot, and it was badly neglected for a couple of summers, resulting in some significant die-back. It lost it's central trunk a few years ago and I cut that down to where the new branches were growing out. At the end of last year I found that the heartwood of the trunk was completely soft and rotted. So I carved-away the soft wood and that ended up creating a bit of a water well down in the living base of the tree. I coated all the exposed wood on the inside with cut paste, but the hole holds water every time it rains or gets watered and I’m worried it will inevitably rot further in the middle and maybe even kill the tree. The tree has otherwise appeared very happy and healthy, pushing new growth like crazy.

I have two ideas for what to do and would very much welcome thoughts and suggestions as this is an otherwise very cool specimen and a VERY vigorous tree that I’ve had for years.

1 - carve through some of the living wood and bark in order to allow the middle to drain water out while waiting for her grow/heal-over the exposed wood areas. In the pictures below, you can see how there is already a spot where the "rim" around the hole takes a long dip downward, so I would take that as the spot to carve-down further. It would need to be carved-down about another inch further to the bottom of that natural notch.
2 - alternatively, maybe I could fill the hole with some kind of wood putty in the hopes that the tree would heal over that, as vigorous as it is, and that wood putty would replace the missing heartwood. I have no idea if that's ok, if it would harm/kill the tree, or what I would use.

Here is a pic of the full tree, showing the vigor in early spring this year (it's been just as vigorous every year);
IMG_3267jpg.jpg

And here is a view of the trunk base and nebari. You can see a barewood span on the nebari, which I have since covered with cut paste and hope it will continue to heal-over. The hole that I'm concerned with in the center of the trunk descends for a couple of inches in the middle of all the green branches you see sprouting out;
IMG_3268jpg.jpg

Here you can see the hole in the trunk base, and the rim of living bark that is healing up around it.
IMG_3264jpg.jpg

Here is a side view of the trunk base showing the natural notch where I am considering carving-down further to allow the center hole to be able to drain. I would need to carve this notch down another inch or more.
IMG_3260jpg.jpg
 

Shibui

Imperial Masterpiece
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No problem filling holes in trees with epoxy putty. New wood will grow over the hardened putty.

I see dead wood at the base as well. The rot will almost certainly continue down through the trunk creating a hollow trunk tree. That will not harm the tree. Lots of trees manage well with hollow trunks. As mentioned above you can just accelerate the process with a drill and let water drain right through
 

Mapleminx

Omono
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