CodingSystemMapping.yml pointing to some deprecated code systems?

[claverols]

Describe the bug
I get warnings about invalid codes when running the current FHIR validator on files I have converted using the latest converter.
When looking at the contents of the CodingSystemMapping.yml included in the HL7toFHIR converter it reads they come from: https://www.hl7.org/fhir/v2/0396/index.html
According to this table they are deprecated?

To Reproduce
Convert an ORU-R01 HL7 message and run the latest FHIR validator (validator_cli.jar). See example attached. Search for references to "code-invalid" within it.
output-oru-r01-sample01-0428.txt

Expected behavior
These warnings should be resolved for the proper conversion of the files.

Desktop (please complete the following information):

• OS: MacOS Big Sur
• Version 11.2.1

Additional context
Some of the warnings mentioned:

"url" : "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-source",
"valueCode" : "TerminologyEngine"
}],
"severity" : "information",
"code" : "code-invalid",
"details" : {
"text" : "None of the codings provided are in the value set http://hl7.org/fhir/ValueSet/report-codes (http://hl7.org/fhir/ValueSet/report-codes), and a coding is recommended to come from this value set) (codes = null#1000)"
},
"expression" : ["Bundle.entry[5].resource.ofType(DiagnosticReport).code"]
},
{
...
{
"url" : "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-source",
"valueCode" : "InstanceValidator"
}],
"severity" : "warning",
"code" : "code-invalid",
"details" : {
"text" : "A code with no system has no defined meaning. A system should be provided"
},
"expression" : ["Bundle.entry[2].resource.ofType(Observation).code.coding[0]"]