Glenn
I just ran a test as follows
I opened my Default Template that has a bunch of Layers, Layers and Layer Groups set up as well as a bunch of View Filters. All my View Filters except one have the switch to disable newly created or imported layers from being added to my View Filters.
I imported a PDF Page and scaled / oriented it
I extracted the vectors from it and created a lot of new layers with the linework
All of my View Filters that had the switch disabled were left intact - the new layers are not visible in those View Filters
The one View Filter where the Disable Switch was enabled had all the newly created Layers and Linework as expected
So I cannot recreate what you are seeing at my end - I guess I need a little video from you and the source data / PDF to see what is going on if you truly have this issue (I have never seen that but you are / were using an older version so this may have been addressed long ago unless you are still seeing this in 4.11).
I did find a couple of issues with PDF Import yesterday that have been addressed for the upcoming Patch - those related to extracted Vector data creating duplicate Layer Names if I have a Template with the Layers already created and assigned to Groups (I was trying to create a Project Template for Michigan DOT Project PDF files (a giant PDF with all the project Data on one PDF (or 3 PDF files) which are all set up in Michigan DOT Layer Standards - so a template with Groups would make managing the data easier - however I found that it just duplicated the layer names (and I thought that this might be what you were seeing in some way) - we also found that if I import a Layer/Groups.Layer file into a project where the Layers already exist the existing Layers did not get Grouped into the imported Group Structure - so we have also amended that today to fix that problem - all other Layer settings (Color, Linestyle, Lineweight etc get left alone, we just update the Group to which the layer is assigned now).
So to follow this up, please provide a PDF File (and the sheet that you are extracting), I will need your Project Template I guess so I am matching to your View Filters etc. and then a short video that demos your Import Process, Settings selected for PDF Extract and the end result showing me the View Filters that are getting updated - the developers tell me that the PDF importer doesn't do anything specific with View Filters so they cannot see how this is happening - I need to be able to reproduce it if they are to act on this issue.
Alan