The problem of different vertex order in blendshapes can be caused for many reasons. For e.g. the topology is same but one of the meshes was edited)
I remember the times when I needed to add extra loops to head with the already created blendshapes. And to not break the vertex order I needed to do all operations in exactly the same sequence for each blendshape. It was a nightmare :)
How can we fix it?
With this add-on you can simply copy and paste verts, edges, faces ids orders between meshes with the same topologies in two clicks in pie menu. Demonstration
Optimized and works really fast!
Сopying and pasting takes about 20 seconds on a mesh with 3 million triangles. On a low poly model, it will take a split second.
Blendshapes is very powerful tool not only for animation but also for modeling and sculpting (morph target technique). Imagine you have a setuped model in Blender with names, materials, textures, applyed but you want to tweak it in some other software. With blendshapes you haven’t to setup from scratch an imported model with changes. You can just use it as blendshape applyed to setuped model. And if it turns out that something wrong with vertex order, you can easily fix it using this add-on.
00| Release v.1.0.7 | Standard Use License | 4 months ago
This worked great on the first try. However it would be great is this wasn't registering any hotkeys (pie menu), or even not using any pie menu at all. Simply accessing the command using search is enough IMHO.
(In other words : the way the tools relies on a pie menu and a hotkey causes a conflict for any user already using alt-t in edit mode ; and the pie and hotkey are not necessary anyways).