Chinese [Topolectical] IPA Placeholder: Ẓ
It's quite clear that there is no difference between "Ẓ" and "ẓ" in the 1987 成都话方言词典 as you have shown. If you look at page 26 of the dictionary, you can see everything that starts with "ẓ" in the particular Chengdu Pinyin system that they have, listed from ẓán to ẓùn. 

Really then, this is a typographical question. Looking at the page, you see that there's plenty of typographical variation, with severe difficulties aligning the underdot of the ẓ below the line. Occasionally, this stretches the verticality of the ẓ character, e.g. in ẓóng,  making it appear a little like a majuscule character where it should be a normal miniscule. 

On a more linguistic level, "ẓ" in this Chengdu Pinyin system corresponds with "r" in the Sichuan Dialect Dictionary 四川方言词典, also published in 1987, although both correspond to   the phoneme /z/. Note that "z" is the romanised version of /ts/ in both, as it is in standard 汉语拼音 too. 

Incidentally, Sichuanese does exhibit the phenomenon of 儿化 érhuà, independently of this phoneme (see 桡片儿 ẓáo pěr in the dictionary). The 成都话方言词典 Chengdu Dialect Dictionary treats them as separate phonemes which happen to be in complementary distribution, whilst the 四川方言词典 Sichuan Dialect Dictionary treats them like 汉语拼音 Hanyu Pinyin does, as realisations of a single /r/ phoneme.