I think you are confusing the terms "program " and "data file". Programs (application software) like PAF and Microsoft Word can use vast numbers of data files (documents). Your PAF data file with 12,000 names is analagous to a word processor document. (You don't need to re-install the program every time you want to start a new file.)
To create a new data file, in PAF's File menu select New and make sure you give the file a NEW name, otherwise it will replace (erase) the existing data file.
You should backup your PAF data files periodically and save backups to various locations such as flash drives, CD/DVD, hard disk, and even as email attachments in messages sent to yourself or to family members. Unless your work is saved to at least 2 different locations, a computer crash could cause it to be lost.