'Program' button or any other option in tool window may disappear from PSoC Designer because of a corrupt XML file related to PSoC Designer. The XML files under "%AppData%\Application Data\Cypress_Semiconductor\PSoC_Designer_51\" store the PD5.1 tool window settings. Removing the files restores the tool window to default settings. Follow the below given steps to restore default settings for PSoC Designer 5.1 SP2:
1. Open My Computer. Make sure PSoC Designer 5.1 is not running.
2. Type %AppData% in explorer address bar
3. Navigate to '..\Application Data\Cypress_Semiconductor\PSoC_Designer_51\'
4. Copy all *.xml files except settings.xml to a newly created temp folder.
5. Delete *.xml files except settings.xml from '..\Application Data\Cypress_Semiconductor\PSoC_Designer_51\'
5. Re-start PSoC 5.1 SP2 and verify if the 'Program' option is available.
6. Delete the temp folder if you are able to see the disappeared button/icon.
If you are facing similar issue in any other version of Designer then follow the similar process as mentioned above but take care of the folder name (PSoC_Designer version) while browsing to the required folder.