Error: frappe.model.utils.link_count.update_link_count exceeded maximum timeout (300 seconds)

You may have hit some sort of tipping point?

So what to increase for a trial period to see what helps:

time out interval
Dropbox backup failed - Job exceeded maximum timeout value - #4 by UmaG

number of workers ERPNext Slow with multiple POS Users - #2 by felix

Also confirm rules of thumb like innodb_buffer_pool_size and other insight from the authority!

https://discuss.frappe.io/search?q=%40rmehta%20innodb