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Would I be able to update the custom module and then put the custom scripts back somehow? I mean if I loose these custom changes, can I put those custom scripts back into this specific module? Hope that makes sense.
Kinda? What customizations did you make?
You can export the existing DataSource to a JSON file which would retain all the changes you made and you can re-import it so it goes right back to how it was. The trick is that you might lose historical data or customized device/instance-level changes doing that. Depending on the customizations you can have LM upgrade the rest of the module without undoing your customization (like if you only changed AppliesTo), or you can just "upgrade" your customized version by manually implementing the changes LM made (like making the groovy code changes). You can also do the opposite in that you just import the new version then re-modify it to redo your customizations.
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