is storage.compact() working ?

Honestly, I'm not sure. Mainly it'll be allocating the string, so:

var evalneed='How much is needed for eval ?';
var cmd = `var x = E.toString(ST.read(".bootcde")); ST.eraseAll(); ST.write(".bootcde",x); console.log("survived");'
if (x===undefined) { throw new Error("Not enough RAM for .bootcde"); }
    else {
evalneed=''; // Required for eval
// Ugly hack !
        eval(cmd);
       // Here i do a reset via my custom watchdog function.
}

would probably be pretty safe.

Or... you could just do:

eval('var x = E.toString(ST.read(".bootcde")); if (x===undefined) throw new Error("Not enough RAM for .bootcde"); ST.eraseAll(); ST.write(".bootcde",x); console.log("survived");');

Which might be tidier/safer?