A few things you can try:
Use FM 4 to recover the original file, then convert the recovered copy.
Save a clone of your 4.1 file and then import all the records from the original copy--this rebuilds all the indexes in the 4.1 file. Then convert this copy to FileMaker 11 format.
Export all the records from the 4.1 file into a tab, csv, excel or other common file format supported by both FMP 4.1 and FMP 11 for import and export. Then save a clone of your converted file and import from this intermediate file.