OverIt – to be fair, I can see two sides to your story.
On the assumption that you’re in NSW, the first side is that whilst the Owners Corporation (of which you’re a member by the way) is responsible for maintaining its Common Property, of which your bathroom window and its seal is a part, they also have the right to obtain their own quotations and engage the tradesperson of their choice to undertake that maintenance, and in a way that doesn’t compromise its building warranty claim.
A possibly allied issue is that the invoice you submitted to your Owners Corporation (O/C) may have been made out to a third-party (i.e. you), in which case some O/C’s and/or Strata Managers will decline payment for reasons of probity.
Clearly the other side is the extenuating circumstance that lead you to, based on your Property Manger’s advice, authorise the necessary repairs to the window and its seal.
If you’re in NSW, your next option is to advise your O/C that you intend to make an Application to the NSW Office of Fair Trading for Mediation, and if that doesn’t elicit the desired response and you want to pursue a “fair and just” outcome after almost 2 years, then read THIS and lodge THIS.