This is an old comments, but other might stumble here.  I have also chosen to use VirtuaWin in the past because I liked how it behaved.  Since Windows 10 introduced Virtual Desktop natively. I decided to give it a a try and favor it, but there was some features missing to make my VD experience as good as I used to know (like VirtuaWin nice little status icon in tray telling you which Virtual Desktop you are located at).  Best solution I found so far is using zVirtualDesktop (https://github.com/mzomparelli/zVirtualDesktop).  It used to be free and open source I believe, however it is now paying.  Might still worth it to encourage the developer, you decide.  I talked to the developer in the past and I can say he is a very nice guy, and I will try to talk to him about reconsidering making it as a free-by-default option (or have a free default behavior and make people that want more pay for example or donate like for RaMMicHaeL's freeware), but that is another story. ;-)

Original anonymous poster is sure not alone to care about this. I came here today specifically for this. ;-) His description and suggestions is way better than the one liner I might have submitted at first.

The main reason I install Taskbar Tweaker on all my Windows installations is to be able to ungroup and be able to re-order and organize my taskbars like I want (i.e., carefully organized at some place). There are reasons people like me and the OP care about this, and losing that order can be painful, etc. (even if we can say: it is not the end of the world, you don't really lose anything, it is reversible, yeap, you are right, but I sure would appreciate this doesn't happen!)

I am the type of user that have dozens... if not hundreds of stuff open (be it tasks, not counting the amount of tabs in each task, e.g., web browser). We can argue it is bad habit, but there are PROs and CONs I can give to it to be honest. Aside from procrastinating or just not cleaning my stuff up, there are good reason I want to keep something open (like: I want to process it but it is not yet processed, and some among these are low priority of course, so they might stay open for a while... until a disaster happen and I lose everything, even if that is very unlikely nowadays with how I evolved my setup and how most software I use save states of what is opened).

You may even be the same as us... but think like you said it is not worth the effort... so the question is, does it requires so much effort?

This comment was however 5 years ago, but looking at some other feedback here RaMMicHaeL, I have saw you said 1 year ago "I might have a piece of code lying somewhere which can save and restore the taskbar items order. Let me know if it can help, and I'll check if I can find it.". I don't know if you ended up using it somewhere, but if that logic exists (or doesn't cost as much to implement as you thought 5 years ago), then the original's poster suggestion to save and restore that order when updating might be a not-so-costly option now and it will keep the orders as we can hope to expect by default IMHO. (We can argue it is a bug or feature [I understand, don't worry], but in an ideal world, if I put my dumb-user hat, I sure don't expect my carefully organized taskbar order to change because I update this utility or anytime actually!).

I also like OP's comment about the save/restore feature that can be used as the basis for other features (at minimum if it crash, even if I don't remember if/when my Taskbar Tweaker crashed!).

P.S., Whether you go ahead and finally do it, or not... I want to THANKS you for providing a nice add-on for free on top of it. Your contribution is really appreciated. I will eventually consider making a small donation and hope everyone appreciating your work do the same.

P.P.S., If you want I give more thought about how we should support this, like save/restore taskbar orders and how this option should be used (and maybe be a new offered feature), I can work on making a small analysis and think this more deeply and carefully consider to keep thing as simple as possible while improving stuff.  Would be a way I can contribute to this nice piece of software.