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As a test, I moved 2 of the affected components out of the browser folder and created a simple rule to just suppress these 2 components. Once I ran this and saved then opened the BOM, the 2 parts had their structure changed to "reference" and they were missing from the parts only list (as expected). Then I created another simple rule to just unsuppress these 2 components again. I ran this and saved and then opened the BOM and they are once again set to "normal" structure and appear as expected in the parts only list.

I then created a new browser folder called "TEST" and moved the 2 components into it. I then created a very simple rule to suppress these parts again in the folder and this time, the parts are suppressed in the model but remain as "normal" structure in the BOM and still appear in the parts only list.

oPane = ThisDoc.Document.BrowserPanes.Item("Model")
oFolder = oPane.TopNode.BrowserFolders.Item("TEST")
oFolderNodes = oFolder.BrowserNode.BrowserNodes

For Each oNode As BrowserNode In oFolderNodes
	oComp = oNode.NativeObject
	oComp.Suppress
Next

If this is true what @chandra.shekar.g says that because it does not work manually then it won't work using iLogic, is there another method to suppress the folder or all of the parts within a folder so that it will work?

I have a lot of components to suppress and unsuppress due to the number of possible configurations and so it is much easier to use folders. However, I need the parts list to accurately reflect the configuration also!