Any new resolution which is adopted by a condominium Board cannot be retroactive (just as no law can be retroactive but can only take effect as of its "effective date"). It's not clear from your posting, but if I've read it correctly, the new definition of "Structural Alteration" is now being attempted to be applied to pre-existing modification by the Board? Such action would be 'ultra vires' (literally, beyond the powers) of the Board, and as such, be both ignorable AND, if the Board pushes it, actionable by the unit owners with preexisting modifications.
Quite often in these condo "HOA Boards" (Home Owners Association), you can get a person who thinks they are entitled to push their opinions onto the rest: talk to the other unit owners who are being threatened and see if they want to hire an attorney jointly. Then that attorney should send a polite but firm letter to the Board advising them that they need to rescind their threatening letters, and acknowledge that no fines are permissible. The big issue is that many of these groups use 'enforcer management companies' who have no problem in then issuing a report to one's credit bureau advising that there is a pending fine- so before this escalates into that kind of problem (which is actionable defamation under Virginia law, to claim that one owes a debt when one does not) see if the put-upon owners can't get someone to talk some sense to the Board.
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I don't see a problem with the actions of the Board of Directors until the last sentence of your question. As for the first part of the question, the BOD has a duty to enforce the terms of the Bylaws or other covenants. The recent resolution appears to clarify the wording of the Bylaws without adding any new requirements. A BOD is usually permitted to make rules which implement the Bylaws, and this seems to be what the BOD was doing.
The problem comes with the attempt to retroactively impose the past violations on current owners for actions taken by prior owners. There could possibly be a provision in the Bylaws which permits this, but that seems unlikely. My suggestion is that the owners who were fined hire a lawyer to fight the assessments. They might be entitled to repayment of any legal fees incurred, under the terms of the Bylaws.
Fairfax -- Annandale -- Falls Church