There are those who use the same files with both Nickel and the alternate readers, and report no problems. That said; I think it is a bad idea, there are too many advantages to hiding the files you want to read with the alternate readers, from the Nickel processing. It is easy to do, just make a folder that starts with a dot/period like .Library, and put your book folders/files into that "hidden" folder. The ebooks are available to the alternate readers, as quickly as it takes your PC to copy them over, no Kobo processing needed. Calibre can use your hidden folder as if it were a drive.
This thread contains some tips that might help.
Luck;
Ken