Is it possible that you can limit the outgoing data like values for Custom Fields only to certain projects.

So adapted to your doc (https://docs.idalko.com/exalate/pages/viewpage.action?pageId=19629012) the outgoing sync of Custom Fields is enabled only on certain projects. e.g.:

Outgoing Sync:
if(issue.project.key == "SD" && issue.type.name == "Bug") {
   replica.customFields. "XY" = issue.customFields. "XY"
   replica.customFields. "XYZ" = issue.customFields. "XYZ"
}
else{
   replica.customFields. "ABC" = issue.customFields. "ABC"
}

So that the values of the custom fields are sent to the other instance only for the project key "SD" and issue type "bug".