One thing I have learned that has made life MUCH easier and I would strongly recommend (because I haven't found a better way to deal with the problem... hint, hint!! )
This problem exists in both the original and the jaBEe editors. When you create a new project and run it, the editor automatically overwrites your existing source code file. This is very very bad because you may forget to restore the backup that is thoughtfully created in the background before making your alternative modification. You can define the number of backup files in the editor, but forget once and you can very very easily lose track of which backup to restore. To test the backup you think "may" be the right one, you have to compile and run it, which in turn creates a new backup. Very VERY confusing imho. (Really wish the editor could compile and run from a backup instead of the main source code file... hint hint!!

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Simple Solution:
Not only will this protect your main source code file from the envasive overwrite, it also make it very convenient to refer back to the original code that you are modifying. These are the steps I use and rules I apply while using the jaPBe (ver 2.4.9.25):
1. Load main source code file, ie. "MyProject.pb"
(You will see your file name on the tab at the top of the document.)
2. Highlight the entire document and copy to the clipboard.
3. Click on the new document "icon" seen just below "File" in the menu bar.
4. Paste your clipboard copy to the empty "New" document that just opened.
5. Modify code in the new document and test until satisfied with changes.
(Here is where it is very handy to click on the tab and refer back to the original code.)
DO NOT PROCEED UNTIL... you are happy with your changes and all is good.
6. Click the tab to bring your original source code page to the top, and close it!
7. Click back to your modified code, Press F12 and save back into the original file name.
8. Return to step 2 above to begin your next modification.
Two Important Rules To Follow:
1. DO NOT give the "New" project a name or save it, accept as noted above!!
2. Modify your code ONLY in the "New" project. Every successfull modification results in the original file being replaced, else you ALWAYS have the untainted original sitting there on the disk to fall back on, as it was before you started. A third benefit is ALL the complimentary auto-backups that are created will be good working code. It may be short one modification, but the procedure above only allows "good working" copies to overwrite your original code file.
This procedure works well for me and "maybe" its the way I was supposed to be doing it from the beginning but, those instructions weren't made apparent to me anywhere. The editor could very easily be made to operate in a similar manner if it would only write to a backup file and compile from there instead of using the main source file. This would allow "the user" to determine when it is appropriate to save and overwrite his own work.
One last thing. I wouldn't want to leave you with the wrong impression. Although I have little experience with the original Purebasic editor, the jaPBe product is very powerful, very efficient, very well layed out and very easy to use. PureBasic is a marvel unto itself. The jaPBe is an extreme compliment to that power and makes it all really easy to harness. Of couse, as you pointed out, the people here are generous so coding is made even easier.