@Ankit Meel (ankitm) I don't believe this is a bug. The small object is being joined to a large object. The large object is the child of the small object and has a different position to the parent.
The objects doesn't disappear, they just shift to the location of the child object which is now "reset" because it no longer has a parent to reference it's location off of.

If you unparent the objects then join them, the issue does not occur.

Always learning and being more attentive. Thank you.

Isn't this behavior to be expected due to the parent inverse matrix? The parent object has moved since it was parented to the child object (verified below) . As a result the child object moves back to its basis transform location when the parenting relationship is broken.

To avoid this quirk of the parent inverse matrix, there are two options:

1. Apply all transforms to the parent with Ctrl+A. This will also reset the parent inverse matrix of child objects
2. Clear Parent and Keep Transformation on the child with Alt+P.

Either way, you then can join objects with the desired result, no need to change to the join operator.

footnote:

# move parent back to it's original location at time of parenting
bpy.data.objects['Slice.006'].matrix_basis = bpy.data.objects['Slice.004'].matrix_parent_inverse.inverted()
#undo the parenting operation
bpy.data.objects['Slice.004'].parent = None

In T76556#930761, @sok0 wrote:

Either way, you then can join objects with the desired result, no need to change to the join operator.

The change is simple anyway, and avoids the need for applying the parent transform first.