How to effectively delete ways in JOSM without removing nodes belonging to other objects/relations

I am trying to remove some old proprietary/conflicting data as a part of a local community campaign initiative, and I cannot figure how to effectively delete ways in JOSM without downloading the whole country.

I have tried to download the data via an overpass query but kept getting warnings of missing referred objects after I deleted the conflicting ways and tried to upload changes.

Next, I compiled a list of ways and nodes IDs from the overpass JSON result, and used the download object function, chose mixed, and passed the list of IDs separated by commas. Now JOSM keeps complaining about node resolution conflicts when I tried to upload changes.

I thought I could just give a list of object IDs that need to be deleted, and JOSM would automatically remove parent relations, and keep nodes that are attached to other objects.

Any pointers would be much appreciated.

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