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This is a follow on to https://ask.openlca.org/1690/importing-some-unit-processes-missing-in-combined-database as Jonas answered that fully (the "missing" processes had the same UUIDs as some already present) but this clarifies the underlying question and might be more helpful.

Datasets (e.g. as .zolca files) can be combined - e.g. by restoring the larger one and then importing the smaller one into it. If some of the processes in the second dataset have the same UUID (identifier) as processes in the first dataset, then they won't be imported. This works and makes sense.

However, some processes in the Ecoinvent 3.5 unit-processes (UP) dataset have the same UUID as their equivalent process in the Ecoinvent 3.5 system-processes (LCI) dataset (I've only been using cut-off). So, when importing the unit-processes dataset into the system-processes dataset, these unit-processes do not get imported.

So, my real question is, what is my best option to use these two datasets (unit and system) together? This seems to be a common thing to do as it enables more transparency of (unit-)processes that are key to a product system while using system-processes as "outer" providers to keep it all computationally efficient. 

Any help in finding a solution would be really appreciated! Many thanks.

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Not sure if I missed something but as far as I can see, equivalent processes in ecoinvent UP/LCI have different UUIDs e.g.:

apple production | apple | Cutoff, U - CN: de20bbdb-364a-30c9-8ee3-14fd22173a80

apple production | apple | Cutoff, S - CN: de4cf6f5-3765-3ae7-a81a-9d6774f777a1

Therefore, you can simply import LCI processes in the UP-based version of ecoinvent.

If for some reason, the UUIDs are the same, you can also assign a new UUID (although this is not really recommended as the chance to cause some problems is probably higher than to actually solve a problem). Maybe you can do this with LCI processes that you want to import as they do not really have links anyway but do not do it with unit processes as the links won't work anymore and definitely create a backup of your database before. And again, this is experimental and not really a recommended practice. Be extremely careful.

Window -> Devloper tools -> SQL

UPDATE TBL_PROCESSES SET REF_ID='NEW UUID' WHERE REF_ID='OLD UUID';

Click on the run button in the top-right corner. Done

Generate UUIDs e.g. via Excel or https://www.uuidgenerator.net/.

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Hi Jonas, Thanks.
My point was not that the approach wasn't consistent in the past (I think it was), just that it didn't help me understand why this would be deliberate - I honestly can't think of an advantage to duplicating UUIDs within a version of Ecoinvent, but that doesn't really matter.
Anyways, I appreciate your time and thanks for answering - I realise you're all very busy but it is great to know that a version with unique UUIDs might happen, even without a timeline. Keep up the great work!
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