While Old Czech had a basic alphabet from which a general set of orthographical correspondences was drawn, it did not have a standard orthography. It also contained a number of sound clusters which no longer exist; allowing ě (/jɛ/) after soft consonants, which has since shifted to e (/ɛ/), and allowing complex consonant clusters to be pronounced all at once rather than syllabically. A phonological phenomenon, Havlik's law (which began in Proto-Slavic and took various forms in other Slavic languages), appeared in Old Czech; counting backwards from the end of a clause, every odd-numbered yer was vocalized as a vowel, while the other yers disappeared.
What kind of orthography was missing from Proto-Slavic?