COS and threshold Salary

Hi Guys, I have a query and would be thankful if someone can help me with this.

I currently hold a 5 year tier 2 visa which I got in July 2019.

I was offered COS by my company under the SOC code 2121 which has a minimum salary requirement of 33000/year (39 hour week). In the COS application, the HR in my company mentioned my salary as 34400 GBP which meant I was within the threshold.

The offer letter the company gave me had the following details:

Basic Pay: 32000 GBP (38 Hours Week) - works out to 32153 (for a 39 hour week)
Employer Pension Contributions: 2400 GBP

I have come to realized that pensions cannot be included as part of gross pay and that means my salary was below the threshold.

However this January I got a pay rise and my basic pay went up to 32800 GBP (38 Hour week). I will also be paid a guaranteed profit share of 3000 GBP for the year. This obviously means my salary is within the threshold.

But, the major issue is the COS salary during my application time. How do I approach this with the home office?