Discussion Forum—A Way with Words, a fun radio show and podcast about language

In English, there're some words that have two spellings and have exactly the same meaning. The words that I want to ask are not those different spellings between British and American English.

These words are as follows:

1. pertinence/pertinency

http://www.merriam-webster.com/dictionary/pertinency

2. subsistence/subsistency

http://www.thefreedictionary.com/subsistency

I just listed four words above. Is there any difference between these words? Is it OK to spell N-encE into N-encY(because almost lots of words have both spelling)?

Thank for your help!