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If you have current plants in your yard the statute of limitations does not even come into play because it is an ongoing alleged violation of the bylaws. HOWEVER, what does come into play is what is called in law the equitable theory of waiver and equitable theory of laches. These equitable theories state that when the HOA ignored enforcing the bylaws and allowed you to expend money and effort and did not stop you for all these years in your gardening, then that failure to act in a reasonable time to enforce the bylaws (which they could have had a right to enforce if they acted timely) amounts to a waiver of enforcement or at least it amounts to their inability to now enforce it after you have done this for so long. They could seek to enforce the bylaw for any future gardening you perform though.
Also, you have a right under the HOA bylaws to file an appeal to the Board and be heard by the board at a meeting to seek to get them to rescind their letter. In addition, if the board refuses to rescind the letter, you can follow the bylaws and propose a bylaw change (if you are in violation of the bylaws) to stop the enforcement and change the bylaw. Finally, if they are not complying with the bylaws or they refuse to rescind, you have a right to then file in court for a declaratory judgment based on the equitable legal principles I stated above to get the court to order that they cannot retroactively enforce the bylaws and can only make you comply in the future (or perhaps even rule that because of their historical non-enforcement they have waived any future rights to enforce that bylaw and the court can invalidate that particular bylaw based on the equitable theory of waiver).
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