Not every IDE upload to the boards works every time,
Not what I experience.
the port numbers swap about on restarts and the output monitor can get confused occasionally.
Fixing the port numbers (better the device file path) is just an UDEV configuration away. There are tons of tutorials about that on the Net.
Which output monitor is meant in that sentence? Was that part of the port numbering problem?
Might hardwired and dedicated serial be more trustworthy (RS232 or RS422)?
How would you connect that to the server? Does your server still has an available RS232 interface? Haven't seen that for years.