System Information
Operating system: Windows 10
Graphics card: 3090 / 3060 / 1050ti

Blender Version
Broken: (Current Builds) (3.0.0 hash: fafd21b14c23, master, 2021-07-22)
Worked: (2.93.1 hash: d6b1d35bf874, master, 2021-07-12)
Caused by rB3b6ee8cee708: Refactor: Move vertex group names to object data

Short description of error

Data copy is deleting vgroup data in 3.0 builds since the 12th.

Exact steps for others to reproduce the error

Running this script deletes the vertex group which began happening in 3.0 builds after the 12th.

import bpy

# all vertices belong to a single group

context = bpy.context
obj = context.object

#get evaluated object
obj_eval = obj.evaluated_get(context.evaluated_depsgraph_get())
print(obj_eval.vertex_groups[:]) #the evaluated object has groups

# and create new mesh from it
new_mesh = bpy.data.meshes.new_from_object(obj_eval)
print(new_mesh.vertices[0].groups[0].weight) # created mesh has groups and weight

# assign new mesh to the object
obj.data = new_mesh
print(obj.vertex_groups[:]) #vertex groups are gone

this example might be more linear

import bpy

context = bpy.context
obj = context.object
print(obj.vertex_groups[:])

# this piece used to preserve vertex groups but it doesn't
obj.data = bpy.data.meshes.new_from_object(obj)
print(obj.vertex_groups[:])

This is what happens in current 3.0 builds.

This is what was happening in 2.93.1LTS and 3.0.0 on the 12th and prior.

Vgroup data was also part of the copy which was expected behavior. The removal of the data is the issue attempting to be outlined.