Will I be able to keep my current save file for future updates when using an external install instead of via Itch?
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Generally, it doesn't matter where you download the zip fle from (e.g, from patreon). The save game is located in a systems folder and would be accessible from any install.
Just make sure to not switch from higher to lower versions or try any "hacked" versions. This can easily kill your savegame.
If you want to use the itch.io app, then make sure to not use the sandbox mode. See this article for more details. https://tinysecretgames.itch.io/snapshot/devlog/1019366/finding-lost-savegame-wh...