Hey Jakub,
Did you copy and paste your variables from your first file to the next?
Keep in mind that, while Variables are still in beta, if you copy and paste objects to different file, the prototype will continue to work as the variables transfer over. However, any unpublished variables applied to prototypes won’t be available for further use, like when creating Set variable actions, or switching an object’s number variable.
We are working on improving transferring variables across files. As a workaround, either recreate the variables in the destination file, or duplicate the original file. If the original file is published to team libraries, copied and pasted variables will work as expected.
If you receive a notification that pasting unpublished variables across files won’t create new local variables yet, try publishing the source library and and enabling it in the destination file.
More details available here:
https://help.figma.com/hc/en-us/articles/14506821864087-Overview-of-variables-collections-and-modes#copy_paste