After the upgrade you should be producing more Iron.
During the upgrade, Mines don’t produce any Iron at all. The same is true for Farms.
The Watchtower, however, will continue producing Iron and Food while upgrading — but only the Watchtower does that; Mines and Farms don’t.
So if your Iron production dropped while your Mines were upgrading, that would be expected.
Did you Iron production go back to normal after your Mines finished upgrading?