Yes, FS to SS, LE to RE, ROLB to LOLB, LG to RG, LT to RT can all be changed in season and the player type will default to whatever scheme they are rated highest in. Problems are that the player type weightings lean heavily towards certain types. e.g. Zone blocking for oline men, speed rusher for DE, cover 2/prototype for LB so makesure to save before you flip a player to change his type incase you don't like the results.
Other positions can be changed in the offseason, e.g. MLB to OLB and back again, HB to FB and back, DT to DE and back, if you want to try and change their types.