X509 signing certificates are used for system signing functionality within the APIs.
Typical uses are signing SAML assertions, tokens, generated PDFs, etc.
A signing certificate is generated for each project, and normally these will not require changing.
You can, however, generate new certificates at any time, or import your own.
X509 encryption certificates are used for when SAML assertions from external IdPs are to be encrypted.
In this case, you supply your encryption certificate to the third party IdP as part of your metadata.
Like signing certificates, you can create a new encrypion certificate, or import an existing one, at any time.
Note
Keys for user signatures are part of the individual user's account