I had two exports going from lightroom cc and the first export window popped up in LRTimelapse 5, but before I could click export, the second timelapse finished rendering in lightroom and that window overrided the first timelapse export window. Now I have to re-export my first timelapse from lightroom again.
First of all, I hope you are talking about Lightroom Classic. What Adobe now calls "Lightroom CC" is the Desktop version of their web-app with reduced feature set which doesn't work with LRTimelapse.
Anyway: any export from Lightroom via LRTExport will end up in its own "LRT_*" folder. After that, the render dialog will be called.
You can activate "Render with last settings" in LRTExport, then it will all happen in one step, without popping up the render dialog.
And in any case, you can always just do "File / Render Video" in LRTimelapse to render any exported intermediate sequence you want. In your case, just do that to render the video clip that is still missing.