Well I have found a solution.
Select all the video files in the project, in your "footage" folder with this issue, then right click and select "Encode selected files". In the next window just click on the preset that you need. Back in the AE project, replace the footage with the new video files that you have just created.
If you see an error window again, don´t worry, the file must work. At least this allow me to modify the project and export it correctly.
I hope this can help to someone.