I highly doubt that messages are actually being deleted from the system - that's rather an expensive affair and not fashionable from state security point of view. For example, if there has been an act of sabotage, having access to those ephemeral messages may be crucial to catch perpetrators.
It's not ideal, but I thought that WeChat had a desktop client (similar to WhatsApp) that allows for slightly easier scrollback, search and export/copy-paste functionality within the group chats. It doesn't help across the wider WeChat platform as the article points out, but in a corporate setting with many adhoc working groups it might help one to maintain context.
This was even more difficult when dealing with clients or third party vendors, because they would have their own WeChat groups where they discussed support issues or purchases. I remember a situation where we had to contact a former employee to find a password to a machine because it had been shared on a chat that only they were on at the time - that sort of thing.
To be fair, I do think that a lot of similar stuff happens on Slack, where private groups get created and decisions are made without always including the correct participants according to the org chart. And probably prior to the explosion of workplace chat apps people were doing this by getting together in person for lunch or drinks or golf. It does make me feel a bit cynical about organizations that claim to hold values of transparency and accountability, though. It seems to me that cliques form regardless, and quietly influence direction regardless of any alleged corporate values.
WeChat, like Whatsapp, stores canonical messages on device and not on the server as opposed to services like Messenger that store messages on the server. It has the same limitations as Whatsapp of only one primary device being able to connect to the service at a time and any new device starting from a blank chat history unless a manual transfer is done.
Some minimal amount of history is stored for government compliance (I believe it's around 30 days but this could have changed) and the government has the ability to flag certain accounts for longer retention but you can be fairly certain that Tencent does not have long term archives of all of your chats, because if they did, they would almost certainly offer chat history across phones.
The disappearance of chats across phones is a major usability pain point of Wechat and something they absolutely would fix if they had the ability but it's a deep technical decision baked in from the early days of the product and the refactor would be non trivial. It also conveniently gets the Chinese government off their back by pointing to a technical reason they can't cooperate to avoid having to deal with the headache of being more deeply enmeshed.
State security concerns aside, deleting messages is less expensive than keeping them. If your plan is to delete everything after N days, it's easy to partition data by day, and then drop the older partitons as needed.