I noticed that under some conditions, my code changes are not being saved if I run the code before manually clicking on the Save button in the editor. My Preferences are set to "Save code to SQL History". I found that if I put the cursor at the top of page, and clicked F9 or the Run icon to run the entire script, I did not have this problem. It only occurs so far if I highlight a portion of the code and Run only that portion. I make a small change in the top portion of remark section, the Select statement and highlighted that portion to execute it. It is discovered after execution, the Save icon is no longer active (grayed-out). However, the change was not saved. One has to manually Save over it with the Save As… function
Manually save the altered query by overwriting it with File |Save As…
Waiting for fix in a future version of SQL Navigator for Oracle .