Hi Michal,
I think the problem is that you use one single model, one big database and that you try to update just a part of your model using Model Update.
That brings several problems and probably the key problem is that for the software there is no difference between objects that were deleted from database and objects that were not selected for comparison/synchnonization.
Example: you have model A with table Customer. During Model Update another model (model B) is created (in fact we need to do reverse engineering to get another model to be able to compare the two models) and in the second model table Customer doesn’t exist. Currently the software is not able to find out why table Customer is missing in the second model. One solution might be in doing reverse engineering of all objects during model update and marking “unselected” items somehow. But I don’t think this would be a solution that will improve your productivity.
Also, there are ways to get the same result already.
I will not recommend you to split your model to smaller parts, for some cases this can be pretty good solution, but I know sometimes it is necessary to manage a model with hundreds of schemas. Let’s take it as a must. What I can recommend you is the following:
A) Keep managing your large model, but instead Model Update do a full RE of your database and then compare just the items you wish to synchronize, like functions for example. In this case, Toad Data Modeler will be able to recognize objects that exist in your original model as well as in the reversed model. Problem of “missing/not-selected” and “missing/deleted” objects would disappear. Also, this way you can keep just one alias for RE with all items selected and without the necessity to use back/forward buttons. And if you do not want to compare logical information, like Notes on functions, this can be easily defined in Sync & Compare Wizard (button Detailed Settings, step Select Object Types).
B) If you wish to compare only functions, create new model and copy/paste there only functions from your original model. Then do RE of your functions and compare the two small models. This might be the fastest and “acceptable” solution (if we take productivity factor into account).
RE version number: I disagree and I bet a lot of Toad Data Modeler users would disagree too. I can imagine that we meet somewhere and discuss it in person. \
Other bugs and improvements: I do not know any software that covers all users expectations and is totally bug-free. I personally tested various high-priced competitive products. If you had the same knowledge/experience you would be surprised 
I’d like to ensure you that we do maximum to bring as many powerful features as possible and fix bugs. BTW: Did you notice that we added to the product some improvements based on your feedback?
Let me apologize for not following up all items in your post - one by one. I think some items will be fixed in future, but now I am not able to say what will appear in next version, what will be removed (in this case I suppose that ideal solution would be in removing model update feature and force you to use improved model merge instead) etc. Thank you for understanding it.
Re alias: some data are stored with alias. This is good if you plan to use the alias with exactly the same settings, otherwise you should create multiple aliases for the same connection. Imagine there are users who has a single model, single database, do changes into a model and forward the changes to database. Only critical changes are made to database first. Model update is in this case a feature that just brings minor changes to exsiting model and is used in scenario whole model-whole database…
Finally let me thank you for your feedback, thank you for the time you spent on reporting TDM features and thank you for all your input.
Have a great day,
Vaclav
