Ok, it looks like removing them from a new model and saving it will accomplish my first question. Apparently I was not doing it right the first few times I tried. Curious if there is a way to just regenerate the default AISC database to "freshen" it up it case I accidentally deleted any members I should not have.

As for my second question it looks like .fil files cannot be modified outside of the program so I am out of luck there.

RISA doesn't give users any way to modify an FIL file outside of the program. Some ways to re-set your FIL file. Depending on your version of the program and where it is installed.
1) If you are using a relatively new version and it is installed into C:\program files\RISA\:
If this is the case then your modified database file exists in your Documents\UserID\RISA\Databases\ folder. However, an original / unmodified version will exist in C:\program files\RISA\databases\. Therefore, you can just copy the the original file from the program files location and overwrite the one in your My Documents folder.

2) If you are using an older version of the program or if it is installed into any folder other than Program Files:
In this case, the program doesn't have an original copy of the file anymore. However, you could still delete the modified FIL file and then re-install the program at which point an unmodified copy could be placed in your folder again.

@azogr
If you don't have the unaltered database, you can just email support@RISA.com and ask them for a copy of the default AISC database. We can email you a copy of the unedited version and you can just replace the current one with it.