Sorry for the lack of clarity on headers and flags, I have not looked these old files and their structure in such depth before, so am discovering and learning as I go. I do like to learn though, so the nerdier part of me is in geek-heaven right now 
There are a lot of Valve ‘approved’ programs and applications out there by third parties, and part of this exploration of the BSP, VMT, VMF, VTF, VPK file structure has revealed in their (perfectly legitimate and endorsed) decompiled states, lots of additional connected files and ‘config files’. These in their own state then have their own sub-structures to them, linking in files from other sub structures.
Overall, I have opened a can of worms and trying to put them back into the can for HammUEr to propagate in UE4 without any texture/mesh/material options is very very very difficult, due to the fragmented state in which the original files are in.
None of this is your fault, but as indicated; matters are made worse when the import process lacks some kind of (intelligent) enumerate system.