So it was not locking up Windows, such that you have to kill power to do anything with the computer; Opus was just taking a long time while the rest of the OS and other applications continued to work? That's a very different situation to what I thought we were talking about before, so what I said above no longer applies.
Synchronize will take a while to gather information about all of the files, especially if you have a very large nested folder structure. It won't read data from inside the files (unless the file display is in a mode which causes that; e.g. displaying thumbnails, or columns like Description, Width or Height which cause file contents to be read). But collating all of the file & folder details can take a while if there is a huge number of files.
For the interactive sync tool (Tools > Synchronize Files), total file size won't matter much (other than inherent overheads of copying the data), but total number of files will. The interactive sync tool in Opus is best suited to small-to-medium folder structures. Half a million files is probably more than I would recommend with that particular tool.
Opus has other types of file synching which are more suited to large folder structures, but won't give you the interactive list of everything that is going to be synched before the sync happens. For example, within the menu attached to the Copy Files button, you can find the Update All and Update Existing commands, which will do a copy from one side to the other and automatically skip files which have not changed. (One will also copy new files, while the other skips new files that have no equivalent in the destination.)
We may improve the interactive sync tool in the future. An alternative, if you want interactive synching of huge folder structures, is to integrate one of the tools which is dedicated to that job into Opus. This can work well, since it will work as a button in Opus which launches the dedicated sync UI between the two folders you are currently displaying. This also gives you diff/merge tools to use directly from Opus for comparing and editing individual files, if you need that.
The External Compare and Merge Tools 2.0 menu provides integrations with various tools. The folder compare ones are what you want here, if you want interactive folder synching. Of the tools that menu supports, KDiff3 and WinMerge are both free and do folder comparisons (although the chart in the post is missing that info for WinMerge; not sure if the menu needs updating to support that). I use Beyond Compare myself, but that one isn't free.