Are you sure that the @target attributes are supposed to be identical to the IDs? Don’t you prepend a pound sign to @target attributes when they point to IDs within the same document?
So you probably need to say

where not(substring($title/@target,2) = $biblStruct) and not(substring($title/@target,2) = $biblFull)

And maybe you need to restrict the titles that you search to those with a @target attribute, like so:

for $title in collection('edil_target/eDIL-A.xml')//entry//title[@target]

Otherwise also non-@target-bearing titles will match the where clause, which may be unintended.

Gerrit

On 25.03.2019 23:32, Chris Yocum wrote:
Hi Markus,

try

for $title in collection('edil_target/eDIL-A.xml')//entry//title
where not($title/@target = $biblStruct) and not($title/@target = $biblFull)
return $title

Thank you for the quick reply at such a late hour!  However, I am
getting the same results sadly.  These results I can open the files
and find the targets that are being return in either of the two lists.

All the best,
Chris

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