This morning I am not having this issue. I have not had it once today so far. It is like a switch turned off.
That said, I reconfigured my avatar to what it was at the time of the bug (captured in video):
MrGreystoneCharacterModel.rbxl (87.6 KB)
I would like to know how to determine if an avatar is using SurfaceAppearance. This one is not, I assume. All avatars used were default roblox configurable. No developer custom SurfaceAppearance Instance containing tools or accessories were inserted.
I am unsure if avatar wearing processes could be related, so I included them here.
This character was created by going to my costumes, and clicking on an R15 costume, and then an R6 costume. The R15 scaling carries over to the R6 option. Everything else is the R6 (body appearance, color, absence of hats):
Though prior, I had this full R15 costume worn, and, that is when I first noticed the issue:

(This character when equipping the tool, partly would flicker (His UpperLeftArm, LowerLeftArm, tended to stay visible the whole time while the (Holding) RightHand, RightUpperHand were almost always flicker prone. Parts closer to the tool handle would disappear more commonly, and all sorts of clusters would partake in the flicker, unlike the captured, where the whole body went. A flickered part would never be farther than an unflickered part; everything that flickered propagated together from the handle.)
I have also repeated the avatar process with different results. ie the action gives incosistent consequence: (may be related)
omitting the last panel (tall repro dude) with the result below (short/default scaling produced version):

(both in the character preview seen here on website and in playing with the avatar, the short option arbitrarily was generated instead with no difference in actions)
this was relieved by dragging the slider to 0 and back to 25, and it returned to the final preview as in the 1->2->3 image.