I am trying to update and remove the picklist value set using tooling api on the basis of active users in the org , i am able to update the picklist value set using json but when it comes to removing the value from ValueSet , i am unable to find any approach .
Sample Code Used While updating the picklist valueset 
 Http h = new Http();
        Httprequest req = new Httprequest();
        string json ='{"Metadata" : {"businessOwnerGroup" : null,"businessOwnerUser" : null,"businessStatus" : null,"caseSensitive" : null,"complianceGroup" : null,'+
    '"customDataType" : null,"defaultValue" : null,"deleteConstraint" : null,"deprecated" : null,"description" : null,"displayFormat" : null,"displayLocationInDecimal" : null,'+
    '"encryptionScheme" : null,"escapeMarkup" : null,"externalDeveloperName" : null,"externalId" : false,"formula" : null,"formulaTreatBlanksAs" : null,"inlineHelpText" : null,"isAIPredictionField" : null,'+
    '"isConvertLeadDisabled" : null,"isFilteringDisabled" : null,"isNameField" : null,"isSortingDisabled" : null,"label" : "PickAUser","length" : null,"lookupFilter" : null,"maskChar" : null,"maskType" : null,'+
    '"metadataRelationshipControllingField" : null,"populateExistingRows" : null,"precision" : null,"readOnlyProxy" : null,"referenceTargetField" : null,"referenceTo" : null,"relationshipLabel" : null,"relationshipName" : null,'+
    '"relationshipOrder" : null,"reparentableMasterDetail" : null,"required" : false,"restrictedAdminField" : null,"scale" : null,"securityClassification" : null,"startingNumber" : null,"stripMarkup" : null,"summarizedField" : null,'+
    '"summaryFilterItems" : null,"summaryForeignKey" : null,"summaryOperation" : null,"trackFeedHistory" : null,"trackHistory" : false,"trackTrending" : false,"translateData" : null,"type" : "Picklist","unique" : null,"urls" : null,'+
    '"valueSet" : {"controllingField" : null,"restricted" : true,"valueSetDefinition" : {"sorted" : false,"value" : [ {"color" : null,"default" : false,"description" : null,"isActive" : null,"label" : "Amanda Deeks","urls" : null,'+
    '"valueName" : "005Dn0000043JTTIA2"}, {"color" : null,"default" : false,"description" : null,"isActive" : null,"label" : "Ben Snowden","urls" : null,"valueName" : "005Dn0000043JTUIA2"},{"color" : null,"default" : false,"description" : null,'+
    '"isActive" : null,"label" : "Caroline Hawkins","urls" : null,"valueName" : "005Dn000003LM7hIAG"}, {"color" : null,"default" : false,"description" : null,"isActive" : null,"label" : "Daniel Hartage","urls" : null,"valueName" : "005Dn0000043JTVIA2"'+
    '} ]},"valueSetName" : null,"valueSettings" : []},"visibleLines" : null,"writeRequiresMasterRead" : null},"FullName" : "Theme_Relation__c.PickAUser__c"}';
    
        req.setHeader('Authorization', 'Bearer' + UserInfo.getUserId());            
        string endpointRemainingUrl = '/services/data/v48.0/tooling/sobjects/CustomField/00NDn00000HiexxMAB';
        string endpoint = Url.getSalesforceBaseUrl().toExternalForm() + endpointRemainingUrl;
        req.setEndpoint(endpoint); 
        req.setHeader('Content-Type','application/json;  charset=utf-8');
        req.setBody(json);
        req.setMethod('PATCH');
        Httpresponse res = h.send(req);