Separate object in corridor

What version of the software are you using?

I use latest version, 10.10.20

A quick scan of the forums mention of IFC export indicate some ongoing issues with IFC export.  If you have access to iTwin design Review, you may have better luck depending on the results you get.   Here's a link to that mention by @markshamoun (Feb 26, 2021)  https://communities.bentley.com/products/road___site_design/f/geopak-inroads-mx-openroads-forum/183734/ifc-export-won-t-work-in-other-software   

The IFC export appears to be entire corridor based as you've noticed, however you can generate multiple corridors using the same alignment.  I recommend creating the two tunnels as their own corridors (each with an independent corridor name).  Utilize the Explorer dialog (OpenRoads Model tab) to help select, add and edit additional corridor objects to these corridors (via right-click menu).  

Feel free to power search google using the following in the google search field:  openroads AND 10.10 AND ifc site:communities.bentley.com

At the moment the workflow that Shawn suggests is also what we have adopted.

As far as we can tell, the problem occurs at the gap between the two objects. ORD is able to process this gap without running into problems as long as you keep the design in the native format. As soon as you export to a different file format however, the gap somehow forces the link between both objects to break.

The problem with the suggested workflow however is that you end up creating a separate corridor for each template drop.

Imagine a corridor that uses two different templates that alternate frequently over a long distance. Instead of one corridor that is easy to manage, you end up with a range of small corridors that require a lot of work to edit constraints, point controls, etc.
And some of the analysis tools such as sight visibility run per corridor, requiring to build a surface before you can run the analysis, again adding more work.

I would really like to export corridors with multiple template drops and different templates to other file formats without losing information en running into problems.

There is no good way to do this but I would export to DGN (remove civil data) then use Microstation Mesh tools to disconnect the meshes by connected faces.

Some info is lost by doing this, Feat Def's for example. So these would need to be reapplied.

If you want IFC export from ORD you need all Meshes to have a Feature Definition, doesn't need to be part of th corridor.

DWG export wouldn't need Feat Defs