How to resolve cells sync errors + conflicts?

Some time ago we migrated from Pydio 8 to Pydio Cells (currently 3.0.3).
Due to the Let’s Encrypt DST Root CA X3 expiration issue the Pydio Sync stopped working for us and we were forced to migrate. This took quite a while, with the result that we “synced” our files manually (by downloading/uploading via web) in that time.
It turned out that our manual sync approach was not very error prone, so we ended up with some conflicts.

We see “conflict on path”, “errors detected while validating patch”, “diff has conflicts [conflict on path]” errors with “Create folder”, “Move folder”, “Transfer File” as “Operations”:


We also would like to avoid syncing “recycle_bin” and the like, but this does not seem to be implemented yet (see: Ignore files/folders + Add support to ignore files/folder · Issue #36 · pydio/cells-sync · GitHub).

We also see “rpc error: code = Internal desc = server closed the stream without sending trailers” which seem to correspond to the following error in the log file:

2021-12-28T23:01:28.204+0100    ERROR   endpoint.cells.remote   Stopping watcher on errorrpc error: code = DeadlineExceeded desc = context deadline exceeded

We also see a zillion CONSOLE LOG false undefined error lines in the log (see: ERROR systray ... CONSOLE LOG [object Object] · Issue #42 · pydio/cells-sync · GitHub):

2021-12-30T12:22:23.498+0100    ERROR   systray http://localhost:3636/static/js/main.6aac3b50.chunk.js?__WB_REVISION__=7d6d77508e11a968d34e:1:59308: CONSOLE LOG false undefined 3 4
2021-12-30T12:22:23.499+0100    ERROR   systray http://localhost:3636/static/js/main.6aac3b50.chunk.js?__WB_REVISION__=7d6d77508e11a968d34e:1:59308: CONSOLE LOG true undefined 1 0
2021-12-30T12:22:23.499+0100    ERROR   systray http://localhost:3636/static/js/main.6aac3b50.chunk.js?__WB_REVISION__=7d6d77508e11a968d34e:1:59308: CONSOLE LOG false undefined 0 1
2021-12-30T12:22:23.499+0100    ERROR   systray http://localhost:3636/static/js/main.6aac3b50.chunk.js?__WB_REVISION__=7d6d77508e11a968d34e:1:59308: CONSOLE LOG false undefined 1 2
2021-12-30T12:22:23.500+0100    ERROR   systray http://localhost:3636/static/js/main.6aac3b50.chunk.js?__WB_REVISION__=7d6d77508e11a968d34e:1:59308: CONSOLE LOG false undefined 1 2
2021-12-30T12:22:23.500+0100    ERROR   systray http://localhost:3636/static/js/main.6aac3b50.chunk.js?__WB_REVISION__=7d6d77508e11a968d34e:1:59308: CONSOLE LOG false undefined 1 2

(If this is something completely different / off-topic, I can create a separate topic on this.)

Anyway, what is the correct way to resolve such sync conflicts / problems? Thanks for your help.