Felix – a hard-line approach with the doors would be around the fact that the Owners Corporation is only required to properly maintain its Common Property, and to renew or replace any fixtures and fittings (such as doors & windows) only where maintenance and/or repair won’t in the O/C’s opinion render such items “serviceable”; such as where the costs of repair exceeds that of a replacement item.
So with that and past situations at your Plan in mind, and if the existing doors and windows in the Lot are serviceable, then your Owners Corporation could refuse to pay the costs of their replacement and to instead consent to the Owner paying for that as part of their proposed renovation.
The magnesite is another story, where I’d recommend waiting until the Report by a Consultant of the O/C’s choosing is received, and from which it can then be determined whether maintenance is in fact necessary in the renovating Owner’s Lot, and if so whether remediation or removal of the magnesite is the recommended solution.
If no maintenance is necessary then the Owner may be given consent by the O/C to themselves remove the magnesite at their cost, and if remediation or removal is recommended, then the O/C should do that at its cost.
By the way, why is a Special By-Law necessary in addition to the passing of a Special Resolution granting the O/C’s consent to the Owner’s proposed renovations? The O/C has already accepted responsibility for the maintenance of balcony doors and windows, so does it wish to make renovating Owner/s responsible for the maintenance of some additional items of Common Property within Lots?