Yes, ἔστιν ἃ is literally “there are which” (“are” not “were"). Cf. εἰσὶν οἳ “there are who” i.e. “there are those who …” or “some people”. The word order is normal. The construction lends itself to various elliptical applications, but here εἷλεν is functioning quite straightforwardly as the verb of the relative clause, and the meaning is simply “and also took a number of towns.”
μετὰ δὲ τῆς Ποτειδαίας τὴν ἀποτείχισιν Φορμίων μὲν ἔχων τοὺς ἑξακοσίους καὶ χιλίους τὴν Χαλκιδικὴν καὶ Βοττικὴν ἐδῄου καὶ ἔστιν ἃ καὶ πολίσματα εἷλεν.
After demolishing the ramparts of Poteideia, having 1600 of Phormions, he devastated Chalcis and Bottika and captured some towns.
This imperfect is problematic to render in Englsih, maybe ‘while devastating Chalcis and Bottika?’
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What has that to do with the question? Anyway, rather “After the blockade of Potidaea, Phormio with his 1600 …”. Phormio was a renowned Athenian commander. For the imperfect, “proceeded to” or “set about” will often do. So “proceeded to lay waste Chalcidice and Bottica and took several towns as well (και).”
“…engaged in despoiling Chalkidike and Bottike and even captured some towns.”
This verb gets used a lot in imperfect. It doesn’t quite come out in the LSJ entry, except the “ravage” gloss, but here in Anabasis 5.5, it’s referring to destruction from an ongoing process of looting:
The “καὶ πολίσματα” here, imo, makes better sense if the mental idea is “plundering.” He wasn’t just stealing everything that wasn’t nailed down, but he even captured some πολίσματα.