So, I think I get your situation now - you're currently Silver and you have until April 22nd to earn 366 more miles to become Gold. If you can't, you'll REMAIN (and not revert) Silver. Since you have an upcoming flight that you can fly on AC, you're wondering if you should credit all flights to A3 and wondering if any miles in excess of the 366 you need will be counted towards requalification (for Gold). My guess is - probably Yes. Since I was Silver long time ago under the old program, I'm not 100% sure but I think it will go something like this. You fly AC on February 5th and after 1 flight you collect the needed 366 miles to upgrade to Gold. Whenever those miles credit, you anniversary date will change (let's suppose it's February 5th). From then on, you have 1 year to fulfill the renewal requirements. Once you get to Gold, the anniversary date doesn't change. But it makes sense that when you're still Blue or Silver, the date changes when you reach a new level. Other airlines with fixed membership years, just give you the status through the end of the current year and the following year. But Aegean doesn't do that.
So, you're faced with a choice - pay for the needed miles to get to Gold now and enjoy the status on your next trip, which will get you lounge access and an extra bag. If you're flying business, you already have that. If you're not, it could be useful but you need to ask yourself, is it going to happen in time - today is the 1st and if you upgrade right away, the Aegean systems will probably recognize your status tomorrow - I have noticed that my account gets updated around noon the day after. So, the A3 system will know you're Gold but you need the *A network to know that, so that you can enjoy those benefits on AC. Not sure that will happen by Monday, the 5th.Thus, I don't advise you to purchase those miles.
Once you get to Gold though, your membership year is fixed. I was from the "old" Golds before Aegean changed the program, so my membership year is from November 24th until November 23rd each year. I just requalified yesterday, so any *A flights I take between now and November 23rd will NOT be carried over to my next qualification year, simply because it hasn't started yet. My balance always gets zeroed out on November 24th. I don't get carryover Tier Miles, I do however have use of the extra award miles but the extra Tier Miles are indeed wasted.
Since you're not Gold just yet, I wouldn't worry about it for now. I hope this has been helpful in making up your mind. Bottom line, any miles earned after you reach Gold, will NOT be wasted as they will be counted towards requalification and I don't think you should spend any money purchasing the missing miles to get you to Gold sooner as I'm not sure you'll be able to enjoy the benefits on your next trip.