Having trouble with Smart Objects "separating" from source PSD

If I understand your problem correctly then try the following: flatten file (edited smart object) then try to save and close.

This is happening when you convert Background layer to Smart Object layer and then you edit it and try to save changes - Photoshop will open window to save file.

Smart objects opened as a separate document for you to work on the object in what ever application the object is associated with. All smart object are not created the same way some have file object like Camera Raw files ,cr2, .nef etc.  others may be a have a vector format like .svg and .ai other are created from a Photoshop Layer or layers.   Other are Placed in image file that are supported by Photoshop.   So when you open a smart object Photoshop created a temp work file for the layer object and passes it to your Operating system to open it in the default associated application.  When the file is closed by what ever application processed it ie ACR, AI or Photoshop. If the files has been updated Photoshop well update the Smart Object layers object the reflect the changes made. If it was not updated the smart object is not updated.

If you process the work document make your changes save and closr the work document.  Photoshop will do the rest and update the Photoshop smart object layers object.

If the Smart object is one that is opened by Photoshop it will become Photoshop active document and if a script that opened the smart object will be active and in control of processing the smart object layers temp work file Photoshop document.  If the smart object temp work file is a Camera RAW File or vector file the will open in Adobe Plug-in ACR or Adobe application Illustrator. The  Script that opened the smart object layers's object will not be able to do the processing of the temp work file. You need to do the in ACR or what ever application the temp work file opens in.

When the document that the smart objects was opened from is closed out of Photoshop, Photoshop will delete the temp work file. Photoshop keeps the work file around to that point in case you re-open the smart object again.  It will not  need to create the work file for it has been create so it can be used again.

If you process the work document in your script you should make the changes you want then save and close the work document.  At that point Photoshop will update the smart object layer object to reflect your changes and your script is still in control of Photoshop.