Warning at 30 seconds is far too late
Perhaps, then again in general, I think a time warning is always kind of arbitrary, and can probably be argued that in most games is mostly just to build up tension to the player, and not really particularly "informative" per se. At the moment of warning the player could be practically a second from finish, or be so far from finish that you might as well restart, and in many games you might not even know yet what's ahead to tell the two case apart.
It may be especially not useful in a Lemmings-like game because time limits (and how forgiving they are) can vary a lot from level to level. 30 seconds might actually be a bit soon for a 1-minute level--you may need to wait a bit even after halfway point before it's good to crank up the release rate.
Blinking text is problematic: We want to emphasize information. The worst we can do is hide that information temporarily, but blink is exactly that. At least blink in different color than transparent.
Haven't seen it myself, but sounds like the transparent portion of the blinking may be too long? You don't need the transparent portion to last very long for the human eye to register. That said, blinking in a different color than transparent is certainly a sensible option.
Some platforming games make your character blink transparently during invincibility frames. Massive problem. Much better to flash in a different color.
Are you thinking of Super Mario? IIRC blinking was only used for the fairly brief moment after the transition from big Mario to small Mario triggered by touching an enemy, where they intentionally allow small Mario a brief moment of not getting further harmed from enemy contact. (Otherwise obviously he would die right away.) It's likely intentional that they chose blinking to depict this, probably to emulate a semi-transparent ghost-like state that would fit the behaviors rather well. Also contrast it with the proper invincibility granted by the invincibility star, which is actually more powerful and grant Mario the ability to kill enemies on touch. That state is depicted by flashing to white or some bright color IIRC.
I've never had problems seeing Mario in that brief transparent-flashing state, even on relatively primitive systems like Nintendo and GameBoy. Perhaps other games do the transparent flashing in worse ways.
I will grant you that objectively speaking, transparent blinking is effectively equivalent to dropping some frames on the animation, so in that sense it is suboptimal, though the degree of impact also depends on how fast the thing is moving.