Java 13 (optionally 8): Decode & Encode partially known / dynamic JSON into classes. Require Jackson.

JSONExample.java

/*
 * Java 13+ (Uses multi-line string).
 * Java 8+ without multi-line string (line 87).
 * Require Jackson dependency (Maven example; Add to <dependencies> in your pom.xml):
 * <dependency>
 *     <groupId>com.fasterxml.jackson.core</groupId>
 *     <artifactId>jackson-databind</artifactId>
 *     <version>2.12.2</version>
 * </dependency>
 */

package org.example;

import com.fasterxml.jackson.annotation.*;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.core.util.DefaultIndenter;
import com.fasterxml.jackson.core.util.DefaultPrettyPrinter;
import com.fasterxml.jackson.databind.ObjectMapper;

import java.util.HashMap;
import java.util.List;
import java.util.Map;


@JsonInclude(JsonInclude.Include.NON_NULL)
@JsonPropertyOrder({"nestedKnownKey"})
class NestedKnownArray {

    @JsonProperty("nestedKnownKey")
    public Integer nestedKnownKey;

    @JsonIgnore
    public Integer excludedKnownKey; // Field sample for internal needs, excluded from JSON processing.

    @JsonIgnore
    private final Map<String, Object> unknown = new HashMap<>(); // All unknown fields go here.

    @SuppressWarnings("unused")
    @JsonAnyGetter
    public Map<String, Object> getUnknown() { // Keep this method for Jackson.
        return this.unknown;
    }

    @SuppressWarnings("unused")
    @JsonAnySetter
    public void setUnknown(String name, Object value) { // Keep this method for Jackson.
        this.unknown.put(name, value);
    }

}


@JsonInclude(JsonInclude.Include.NON_NULL)
@JsonPropertyOrder({"topKnownKey", "nestedKnownArray"})
class Top {

    @JsonProperty("topKnownKey")
    public Integer topKnownKey;

    @JsonProperty("nestedKnownArray")
    public List<NestedKnownArray> nestedKnownArray = null;

    @JsonIgnore
    public Integer excludedKnownKey; // Field sample for internal needs, excluded from JSON processing.

    @JsonIgnore
    private final Map<String, Object> unknown = new HashMap<>(); // All unknown fields go here.

    @SuppressWarnings("unused")
    @JsonAnyGetter
    public Map<String, Object> getUnknown() { // Keep this method for Jackson.
        return this.unknown;
    }

    @SuppressWarnings("unused")
    @JsonAnySetter
    public void setUnknown(String name, Object value) { // Keep this method for Jackson.
        this.unknown.put(name, value);
    }

}


public class JSONExample {

    public static void main(String[] args) throws JsonProcessingException {
        final String jsonStr = """
            {
                "topKnownKey": 1,
                "topUnknownKey": 2,
                "nestedKnownArray": [
                    {
                        "nestedKnownKey": 3,
                        "nestedUnknownKey": 4
                    },
                    {
                        "nestedKnownKey": 5,
                        "nestedUnknownKey": 6
                    }
                ],
                "nestedUnknownArray": [
                    {
                        "nestedKnownKey": 7,
                        "nestedUnknownKey": 8
                    }
                ]
            }
            """;

        // Decode.
        ObjectMapper om = new ObjectMapper();
        Top top = om.readValue(jsonStr, Top.class);

        // Modify.
        top.topKnownKey = 100;
        top.excludedKnownKey = 200;
        top.nestedKnownArray.get(0).nestedKnownKey = 300;
        top.nestedKnownArray.get(0).excludedKnownKey = 400;

        // Encode.
        DefaultPrettyPrinter pp = new DefaultPrettyPrinter();
        pp.indentArraysWith(DefaultIndenter.SYSTEM_LINEFEED_INSTANCE);
        String jsonStrOut = om.writer(pp).writeValueAsString(top);

        // Print output.
        System.out.println(jsonStrOut);
    }

}