This is a poor behavior by the software and something they should fix. It may be best to generate a new project in the location you want. Then copy the schematic and PCB files there from Windows and then add them as existing documents. Then regenerate the project.
If you want to risk it, back up your project first and then edit the PrjPCB file in a text editor and look for the text "DocumentPath" key name that has the old path names. Deleted the value (but leave the key name and the = sign) and then save the file and perhaps close and reopen the project within CS. If when you migrated the project you copied the *.PrjPCB file and renamed or save it as another name it still gets remnants of the older file structure and path names. My guess is there is the old path name still there.
How CS handles the output files and folders remains a mystery to me. It seems to generate an *.outjob type file sometimes and sometimes not. That might be because it found the outjob file someplace else off the old path name that is still in the project file.
In my case it always saves some of the output files into a folder named Default Configuration. Even if I change the path to something else such as a folder named Outputs it will always put the schematic PCB files in Default Configuration (sigh). When marketing decides to change the product name as suits their whims of the day they want the new docs to reflect the project name change too. It is always a pain (end of mini-rant).
I found this thread that has a method of copying the projects.
It is a start but might not work for everyone. One thing I notice is that you can have the schematic and PCB files directly in the directory/folder structure with the project file or they can be shortcut links to files that are elsewhere. This is evident by the way CS shows the icon next to the files in the Source Documents list in the project tab. It is my guess that it is probably better to have the schematic, PCB, local libraries and other project specific files in the local project folder to simplify path names.
I agree. Creating a new project seems to resolve most of the issues that are created. Before you spend the time, first try creating a new *.outjob file. You can delete the original or move it or rename it. Honestly, I doubt this will fix it but it's simple and you can try it.
You might also want to look at Output generation error: error ocurred deleting previous output Not quite the same issue but probably related (and for whatever reason I have not seen it happen in a long time now).
I'm currently needing to generate output files for a design in circuit studio. Generally this is no problem on other projects, but on one particular file it gets an error looking for a directory on a computer that belonged to a previous designer who is no longer with the company (see below) and then sticks trying to generate outputs, even when I de-select any *.pdf type outputs, see further below, and it still tries to product the outputs - NOTE the 'running' status next to items that are unchecked.
I have gone into options and checked the output folders are all local to my machine, I've saved the project, shut down CS , rebooted and re-started CS and it's still doing it.
I need to generate files for manufacture ASAP so your earliest attention and resolution would be appreciated.