Please follow the MicroStation Programming forum best practices.
Identify Your Platform
Please identify the version of MicroStation, or other product such as PowerDraft, that you are using: MicroStation CONNECT or MicroStation V8i. What is the 8-digit version number (e.g. 10.xx.yy.zz) of MicroStation?
If you're using MicroStation in a ProjectWise (PW) managed environment, let us know that too.
The APIs supplied with MicroStation CONNECT are different to those supplied with MicroStation V8i. Consequently, our answers are likely to be different.
MDL Development
[quote user="jeff.clough"]We have an MDL application ported to Native Code[/quote]
So far, so good! But tell us what platform you are using.
[quote user="jeff.clough"] I am adding the custom linestyle to the element descriptor (and validating it is there via mdlElement_hasLineStyle()[/quote]
Code Syntax Highlighting
When you post code, use the Forum advanced editor's syntax highlighting tool. That's the icon that resembles a pencil: 
[quote user="jeff.clough"] I understand that this issue is likely caused by the reference file not having the custom linestyle definitions loaded[/quote]
If the hosting application is MicroStation (which, as Jan writes, you haven't actually told us), then MicroStation has opened and owns any required resources. If you think about it, how would a reference file (a piece of read-only data) load anything?