Version 12 was a major upgrade from 11 and 13 added on to 13. 11 databases (fp7) have to be converted to 13 format (fmp12), Filemaker will automatically make a new converted file without deleting your fp7 file. Filemaker 12 introduced themes which has really been expanded in 13. You may run in to some visual problem on your layout withs item not converting correctly. You may want to move one databases at a time and make sure it runs and appears as it should. It wouldn't be fun to have to rush fix 20+ database at one time. You might also consider downloading a trail version of 13 and test a couple databases. http://info2.filemaker.com/Global_Individual_FileMaker_Trial_Registration.html?
Yet converting a set of FMP 11 files that are linked with external data source references would best be done converting them all in one group as that will help keep the EDS references functional in the converted copies of your original files.