Can I carry over the invention file reference to the patents?

No. Not exactly. In Continux, each file reference is globally unique and cannot be reused. 

However, you can of course use a family root reference and add a suffix for inventions, for example INV. Example: Project_Alpha1_INV. 

If the invention later becomes a patent, you can keep the root of the file reference and only change the suffix. Example: DE national patent: Project_Alpha1_DE or EP patent: Project_Alpha1_EP, and so on.