Workflow needs workover

Changing a workflow takes too long (16h) and other processes can interfer (automatic backup).
Because of the interferance the new workflow wasn't activated and most of the issues were converted to the new workflow (nobody could change these issues to resolved, closed, ...) I'm told that you need to redo the workflow change until all issues are converted (but if this takes 16 h everytime then it's not worth the trouble). So for everybodies sake I had to restore a backup to get everything going again.

It seems the workflow activation needs a workover to improve its speed and to ensure that nothing can interfere while it's running.
It seems there's a missing indirection because every issue has to be changed when the workflow changes.
The workflow only consists of a little amount of steps. If you put something between the issue and the workflow then you should be able to change it in a few seconds and see problems when there are missing steps that can't convert. Normally you add stuff to a workflow so there shouldn't be a need to change the issue because all the steps that where in the previous workflow are also in the new workflow

Also there is nothing in the log or on the screen that gives you an indication what's going on or wrong or if it succeeded, ...

Documentation for the prof. edition only states how to activate a workflow (It wasn't hard to adjust but is this really all, no warnings that it takes allmost a day, that other processes will interfer)