Method 3 (Recommended):

Move the characters off the encounter board and delete the encounter board with all its contents. Save the workshop as the RPG Framework. Then create separate workshops with only the encounter content (without characters) without the framework. To play an encounter, load the empty RPG Framework workshop and then use the "Additive Load" option to load the desired encounter content. Once the encounter is complete, you can delete the encounter board with all its content (which will preserve all other objects like hit point tokens and spells cards). Now the workshop is content empty again, ready to "Additive Load" the next encounter.

Method 2:

Create side tables with a encounter board for each encounter. Use Fog of War or Hidden Area to hide these side tables from other players. Lift the current encounter board with all contents on it and place it on a empty side table. Take the desired replacement encounter board and move it to the play table.

This method theoretically works but I find that sometimes the contents are not properly lifted with the encounter board and they "fall through". This solution also means that the contents of the encounter board cannot be locked (or at least need to be unloaded) before moving.

Method 1 (Brute Force):

Save each encounter as a separate game and after finishing each encounter, load then next encounter game and manually set up the common game objects (hit point tokens, spell cards, etc) to match the state at the end of the previous encounter.

This method works but it least desirable because it means adjusting objects manually at the beginning of each encounter to match the end of the previous encounter.