Prior to v126.96.36.199 we defaulted to SHA-1 signatures.
Later versions default to SHA-256 signatures although SHA-1 is still supported.http://www.componentspace.com/Forums/5316/SHA1-vs-SHA256-XML-signatures
Upgrading your PFX file to the correct CSP should not affect other integrations.
The only change made to the PFX is a property that specifies which CSP to use.
The rest of the PFX, including the private key, remain unchanged.
You can still use the PFX to generate SHA-1 signatures if required.
Also, partner sites with your CER file can continue to use the same CER file.